gmx_MMPBSA.py的安装及使用--只翻译部分内容，具体可参考官方文档(https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/)
聂琨
程序
gmx_MMPBSA：主程序，执行计算功能gmx_MMPBSA_ana：图形界面分析数据并保存高质量图片gmx_MMPBSA_test：测试
环境
GROMACS：version 4.x.x or 5.x.x or 20xx.xAmberTools：20 or 21Python3
安装
两种安装方式：conda environment AmberTools compilation
1. conda
conda create -n gmxMMPBSA python=3.9 -y -q
conda activate gmxMMPBSA
conda install -c conda-forge mpi4py=3.1.3 ambertools=21.12 compilers -y -q
python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
#optional,if want to use gmx_MMPBSA_ana
python -m pip install pyqt5
# Optional
conda install -c bioconda gromacs==2021.3 -y -q
python -m pip install gmx_MMPBSA
2. Ambertools
amber.python -m pip install git+https://github.com/Valdes-Tresanco-MS/ParmEd.git@v3.4
amber.python -m pip install gmx_MMPBSA Input files
| Force field | Structure | Index | Trajectory | Topology | Reference Structure | Small Molecule Mol2 |
|---|---|---|---|---|---|---|
| AMBER | tpr,pdb | ndx | xtc,trr,pdb | optional | Optional | Only if not top defined |
| CHARMM | tpr,pdb | ndx | xtc,trr,pdb | Always | Optional | No |
Usage
Running
# mmpbsa.in输入文件的创建见下文
mpirun -np 2 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md.tpr -ci index.ndx -cg 1 13 -ct md.xtc -cp topol.top
or
gmx_MMPBSA -O -i mmpbsa.in -cs md.tpr -ci index.ndx -cg 1 13 -ct md.xtc -cp topol.topInput Samples
# GB
&general
startframe=5, endframe=100, interval=5, verbose=2,
forcefields="oldff/leaprc.ff99SB,leaprc.gaff"
/
&gb
igb=5, saltcon=0.150,
/
&decomp
idecomp=2, dec_verbose=3,
# This will print all residues that are less than 4 Å between
# the receptor and the ligand
print_res="within 4"
/
# QM/MMGBSA
&general
startframe=5, endframe=100, interval=5,
/
&gb
igb=5, saltcon=0.100, ifqnt=1,
qm_residues="A/240-251 B/297", qm_theory="PM3"
/
# PB
&general
startframe=5, endframe=100, interval=5,
forcefields="oldff/leaprc.ff99SB,leaprc.gaff"
/
&pb
istrng=0.15, fillratio=4.0
/
# MMPBSA with membrane proteins
&general
startframe=1, endframe=100, interval=1,
/
&pb
memopt=1, emem=7.0, indi=4.0,
mctrdz=-10.383, mthick=36.086, poretype=1,
radiopt=0, indi=4.0, istrng=0.150, fillratio=1.25, inp=2,
sasopt=0, solvopt=2, ipb=1, bcopt=10, nfocus=1, linit=1000,
eneopt=1, cutfd=7.0, cutnb=99.0,
maxarcdot=15000,
npbverb=1,
/
# MM/3D-RISM
&general
startframe=20, endframe=100, interval=5,
/
&rism
polardecomp=1, thermo="gf"
/
# Alanine scanning
&general
startframe=5, endframe=21, interval=1,
forcefields="oldff/leaprc.ff99SB", PBRadii=4
/
&gb
igb=8, saltcon=0.150, intdiel=10
/
&alanine_scanning
mutant='ALA', mutant_res='B:12'
/
# Decomposition analysis
&general
startframe=5, endframe=21, interval=1,
/
&gb
igb=5, saltcon=0.150,
/
&decomp
idecomp=2, dec_verbose=3,
# This will print all residues that are less than 4 Å between
# the receptor and the ligand
print_res="within 4"
/
# Entropy with NMODE
&general
startframe=5, endframe=21, interval=1,
temperature=298
/
&gb
igb=2, saltcon=0.150,
/
&nmode
nmstartframe=10, nmendframe=21, nminterval=2,
maxcyc=50000, drms=0.0001,
/
# Interaction Entropy
&general
startframe=5, endframe=21, interval=1,
# Interaction Entropy (IE)
# (https://pubs.acs.org/doi/abs/10.1021/jacs.6b02682) approximation
forcefields="oldff/leaprc.ff99SB",
interaction_entropy=1, ie_segment=25,
temperature=298,
/
&gb
igb=2, saltcon=0.150,
/命令行
$ gmx_MMPBSA -h
usage: gmx_MMPBSA [-h] [-v] [--input-file-help]
[--create_input [{gb,pb,rism,ala,decomp,nmode,all}]
[-O] [-prefix <file prefix>] [-i FILE] [-xvvfile XVVFILE] [-o FILE]
[-do FILE] [-eo FILE] [-deo FILE] [-nogui] [-s] [-cs <Structure File>]
[-ci <Index File>] [-cg index index]
[-ct [TRJ [TRJ ...]]] [-cp <Topology>] [-cr <PDB File>]
[-rs <Structure File>] [-ri <Index File>] [-rg index]
[-rt [TRJ [TRJ ...]]] [-rp <Topology>] [-lm <Structure File>]
[-ls <Structure File>] [-li <Index File>] [-lg index]
[-lt [TRJ [TRJ ...]]] [-lp <Topology>] [--rewrite-output] [--clean]
optional arguments:
-h, --help # 显示帮助界面
-v, --version # 打印版本
--input-file-help # 打印输入文件内的所有选项 (default: False)
--create_input # 创建选定计算类型的输入文件 (default: None)
# [{gb,pb,rism,ala,decomp,nmode,all}]
Miscellaneous Options:
-O, --overwrite # 输出文件覆盖输出(default: False)
-prefix <file prefix> # 中间文件的命名格式 (default: _GMXMMPBSA_)
Input and Output Files:
-i FILE # MM/PBSA input file. (default: None)
-xvvfile XVVFILE XVV file for 3D-RISM.
-o FILE # 输出数据文件 (default: FINAL_RESULTS_MMPBSA.dat)
-do FILE # 能量解构输出文件 (default: FINAL_DECOMP_MMPBSA.dat)
-eo FILE # 每帧的不同能量项输出到csv文件 (default: None)
-deo FILE # 输出每个残基的解构能量项到csv文件 (default: None)
-nogui # 在所有计算结束后不打开 gmx_MMPBSA_ana (default: True)
-s, --stability # Perform stability calculation.(default: False)
-cs <Structure File> # 复合物的结构文件(default: None)
-ci <Index File> # 复合物的index文件 (default: None)
-cg index index # 蛋白 配体的index (default: None)
-ct [TRJ [TRJ ...]] # 复合物轨迹 确保轨迹已经fitted 和 消除周期性 (default: None)
-cp <Topology> # 复合物topol (default: None)
-cr <PDB File> # 参考结构(default: None)
-rs <Structure File> # 受体结构 (default: None)
-ri <Index File> # Index file of the unbound receptor. (default: None)
-rg index # 受体index (default: None)
-rt [TRJ [TRJ ...]] # 受体轨迹 (default: None)
-rp <Topology> # 受体轨迹 (default: None)
-lm <Structure File> # 配体mol2文件(default: None)
-ls <Structure File> # 配体结构文件 (default: None)
-li <Index File> # 配体index文件 (default: None)
-lg index # 配体index (default: None)
-lt [TRJ [TRJ ...]] # 配体轨迹 (default: None)
-lp <Topology> # 配体topol (default: None)
-rewrite-output # Do not re-run any calculations, just parse the output
# files from the previous calculation and rewrite the
# output files. (default: False)
--clean # 清除缓存文件 (default: False)gmx_MMPBSA --create_input [gb|pb|rism|ala|decomp|nmode|all] 输出预设的输入文件Namelist
&general
sys_name (default=none) 定义系统名
startframe (Default = 1) 起始帧
endframe (Default = 9999999) 终止帧
interval (Default = 1) 帧间隔
forcefields (Default = "oldff/leaprc.ff99SB,leaprc.gaff")
| Name | Description |
|---|---|
| "oldff/leaprc.ff99" | ff99 for proteins and nucleic acids |
| "oldff/leaprc.ff03" | ff03 (Duan et al.) for proteins and nucleic acids |
| "oldff/leaprc.ff99SB" | ff99SB for proteins and nucleic acids |
| "oldff/leaprc.ff99SBildn" | ff99SB modified for the "ILDN" changes for proteins and nucleic acids |
| "oldff/leaprc.ff99bsc0" | ff99SB force field using parmbsc0 for nucleic acid |
| "leaprc.protein.ff14SB" | ff14SB only for proteins |
| "leaprc.protein.ff19SB" | ff19SB only for proteins |
| "leaprc.DNA.bsc1" | ff99bsc0+bsc1 only for DNA |
| "leaprc.DNA.OL15" | ff99bsc0+OL15 only for DNA |
| "leaprc.RNA.OL3" | ff99bsc0_chiOL3 only for RNA |
| "leaprc.gaff" | General Amber Force Field for organic molecules |
| "leaprc.gaff2" | General Amber Force Field 2 for organic molecules |
| "leaprc.GLYCAM_06j-1" | Glycam_06j-1 carbohydrate ff (Compatible with ff12SB and later) |
| "leaprc.GLYCAM_06EPb" | GLYCAM-06EPb carbohydrate ff (Compatible with ff12SB and later) |
| "gmxMMPBSA/leaprc.GLYCAM_06h-1" | * GLYCAM-0606h-1 carbohydrate ff (Compatible with ff99SB and earlier) |
| "gmxMMPBSA/leaprc.zaa99SB" | * Force field for Zwitterionic amino acids (Compatible with ff99SB) |
protein_forcefield 定义蛋白力场参数(removed v1.5)
ligand_forcefield 定义配体力场参数(removed v1.5)
ions_parameters (Default = 1)定义离子参数
1: frcmod.ions234lm_126_tip3p (Li/Merz ion parameters for +2 to +4 ions in TIP3P water (12-6 normal usage set))
2: frcmod.ions234lm_126_spce (same, but in SPC/E water)
3: frcmod.ions234lm_126_tip4pew (same, but in TIP4P/EW water)
4: frcmod.ions234lm_hfe_tip3p (Li/Merz ion parameters for +2 to +4 ions in TIP3P water (12-6 HFE set))
5: frcmod.ions234lm_hfe_spce (same, but in SPC/E water)
6: frcmod.ions234lm_hfe_tip4pew (same, but in TIP4P/EW water)
7: frcmod.ions234lm_iod_tip3p (Li/Merz ion parameters for +2 to +4 ions in TIP3P water (12-6 IOD set))
8: frcmod.ions234lm_iod_spce (same, but in SPC/E water)
9: frcmod.ions234lm_iod_tip4pew (same, but in TIP4P/EW water)
10: frcmod.ionslm_126_opc (Li/Merz ion parameters for -1 to +4 in OPC water (12-6 normal usage set))
11: frcmod.ionslm_hfe_opc (Li/Merz ion parameters for -1 to +4 in OPC water (12-6 HFE set))
12: frcmod.ionslm_iod_opc (Li/Merz ion parameters for -1 to +4 in OPC water (12-6 IOD set))
13: frcmod.ions1lm_126_tip3p (Li/Merz ion parameters for +1 and -1 ions in TIP3P water (12-6 normal usage set))
14: frcmod.ions1lm_126_spce (same, but in SPC/E water)
15: frcmod.ions1lm_126_tip4pew (same, but in TIP4P/EW water)
16: frcmod.ions1lm_iod (Li/Merz ion parameters for +1/-1 ions in TIP3P, SPC/E, and TIP4P/EW waters (12-6 IOD set))
PBRadii (Default = 3) 设置PBradii
1: bondi, recommended when igb = 7
2: mbondi, recommended when igb = 1
3: mbondi2, recommended when igb = 2 or 5
4: mbondi3, recommended when igb = 8
5: mbondi_pb2
6: mbondi_pb3
7: charmm_radii
temperature (Default = 298.15) 指定计算温度
qh_entropy (Default = 0) 是否执行quasi-harmonic entropy(QH)近似
interaction_entropy (default = 0) 是否执行interaction entropy(IE)近似
ie_segment (Default = 25) 最后25%的轨迹计算IE
c2_entropy (default = 0) 是否执行C2 Entropy近似
assign_chainID (Default = 0)
exp_ki (Default = 0.0)
full_traj (Default = 0) 是否打印所有轨迹(1)
gmx_path 指定gmx路径
keep_files (Default = 2) 指定保存文件
0: Keep only Hierarchical Data Format (h5) file
1: Keep all temporary files (prefix*)*
2: Keep all temporary files (prefix) and Hierarchical Data Format (h5) file
netcdf (Default = 0) 是否使用netcdf文件代替临时ACSII文件，默认不使用。使用netcdf文件将加速大轨迹的计算
solvated_trajectory (Default = 1) 是否生成无水和离子的干净轨迹（1为生成）
verbose (Default = 1) 指定输出信息量
0: Print only difference terms
1: Print all complex, receptor, ligand, and difference terms
&gb
igb (Default = 5) Generalized Born method to use
1: The Hawkins, Cramer, Truhlar pairwise GB model (GB-HCT)
2: Modified GB model 1 developed by A. Onufriev, D. Bashford and D.A. Case (GB-OBC1)
5: Modified GB model 2 developed by A. Onufriev, D. Bashford and D.A. Case (GB-OBC2)
7: GBn model described by Mongan, Simmerling, McCammon, Case and Onufriev (GB-Neck)
8: Same GB functional form as the GBn model (igb=7), but with different parameters. Developed by Nguyen, Pérez, Bermeo, and Simmerling (GB-Neck2)
alpb (Default = 0)
使用 Analytical Linearized Poisson-Boltzmann (ALPB) 近似处理隐式溶剂的静电相互作用
arad_method (Default = 1)估计分子有效经典尺寸/半径的方法
1: Use structural invariants
2: Use elementary functions
3: Use elliptic integral (numerical)
intdiel (Default = 1.0) 定义内部介电常数.
extdiel (Default = 78.5) 定义外部介电常数.
saltcon (Default = 0.0) 盐浓度(M)
rgbmax (Default = 999.0) 计算有效GB半径的距离截断
surften (Default = 0.0072) 表面张力值Units in kcal/mol/Å2
surfoff (Default = 0.0) 非极性对溶剂化自由能项的贡献值的校正值
molsurf (Default = 0) 计算非极性溶剂化项的表面积
0: LCPO (Linear Combination of Pairwise Overlaps)
1: molsurf algorithm
msoffset (Default = 0) 计算 molsurf 表面时应用于系统中单个原子半径的偏移量。
probe (Default = 1.4)探针分子的半径（以 Å 为单位）（假定为溶剂分子的大小），用于确定分子表面。
ifqnt (Default = 0) 定义是否使用QM
0: Potential function is strictly classical
1: Use QM/MM
qm_theory 使用那种半经验方法
PM3, AM1, MNDO, PDDG-PM3, PM3PDDG, PDDG-MNDO, PDDGMNDO, PM3-CARB1, PM3CARB1, DFTB, SCC-DFTB, RM1, PM6, PM3-ZnB, PM3-MAIS, PM3ZNB, MNDO/D, MNDOD. The dispersion correction can be switched on for AM1 and PM6 by choosing AM1-D* and PM6-D, respectively. The dispersion and hydrogen bond correction will be applied for AM1-DH+ and PM6-DH+.
qm_residues 指定qm残基
qmcut (Default = 9999.0) qm/mm电荷相互作用截断
scfconv (Default = 1.0e-8) SCF收敛标准 (kcal/mol).
writepdb (Default = 1)输出qm区域pdb
0: Don't
1: Write a PDB file of the selected QM region
peptide_corr (Default = 0) 对肽键进行分子力场校正
0: Don't
1: Apply a MM correction to peptide linkages
verbosity (Default = 0) 控制qm输出详细程度
0: only minimal information is printed - Initial QM geometry and link atom positions as well as the SCF energy at every ntpr steps.
1: Print SCF energy at every step to many more significant figures than usual. Also print the number of SCF cycles needed on each step.
2: As 1 and also print info about memory reallocations, number of pairs per QM atom, QM core - QM core energy, QM core - MM atom energy, and total energy.
3: As 2 and also print SCF convergence information at every step.
4: As 3 and also print forces on the QM atoms due to the SCF calculation and the coordinates of the link atoms at every step.
5: As 4 and also print all of the info in kJ/mol as well as kcal/mol.
&pb
ipb (Default = 2) pb模型设置介电模型
0: No electrostatic solvation free energy is computed.
1: The dielectric interface between solvent and solute is built with a geometric approach.
2: The dielectric interface is implemented with the level set function. Use of a level set function simplifies the calculation of the intersection points of the molecular surface and grid edges and leads to more stable numerical calculations.
4: The dielectric interface is also implemented with the level set function. However, the linear equations on the grid points nearby the dielectric boundary are constructed using the IIM. In this option, The dielectric constant do not need to be smoothed, that is, smoothopt is useless. Only the linear PB equation is supported, that is, npbopt = 0. Starting from the Amber 2018 release, solvopt is no longer relevant as only one stable solver is supported.
6: The dielectric interface is implemented analytically with the revised density function approach (sasopt = 2). The linear equations on the irregular points are constructed using the IIM and fully utilizing the analytical surface. Otherwise, it is exactly the same as ipb = 4.
7: The dielectric interface is implemented analytically with the revised density function approach (sasopt = 2). The linear equations on the irregular points are constructed using the Χ-factor harmonic average method.
8: The dielectric interface is implemented analytically with the revised density function approach (sasopt = 2). The linear equations on the irregular points are constructed using the secondorder harmonic average method.
inp (Default = 2) 计算非极性溶剂自由能的方法
1: The total non-polar solvation free energy is modeled as a single term linearly proportional to the solvent accessible surface area. If inp = 1, use_sav must be equal to 0.
2: The total non-polar solvation free energy is modeled as two terms: the cavity term and the dispersion term. The dispersion term is computed with a surface-based integration method closely related to the PCM solvent for quantum chemical programs. Under this framework, the cavity term is still computed as a term linearly proportional to the molecular solvent-accessible-surface area (SASA) or the molecular volume enclosed by SASA.
sander_apbs (Default = 0) 是否使用apbs进行计算
indi (Default = 1.0) 内部介电常数 This corresponds to epsin in pbsa.
exdi (Default = 80.0) 外部介电常数This corresponds to epsout in pbsa.
emem (Default = 4.0) 设置膜介电常数 This corresponds to epsmem in pbsa.
smoothopt (Default = 1)指示 PB 如何为位于溶质/溶剂介电边界上的有限差分网格边缘设置介电值。
0: The dielectric constants of the boundary grid edges are always set to the equal-weight harmonic average of indi and exdi.
1: A weighted harmonic average of indi and exdi is used for boundary grid edges. The weights for indi and exdi are fractions of the boundary grid edges that are inside or outside the solute surface.
2: The dielectric constants of the boundary grid edges are set to either indi or exdi depending on whether the midpoints of the grid edges are inside or outside the solute surface.
istrng (Default = 0.0) 离子强度(M)
radiopt (Default = 1) 设置原子半径
0: Use radii from the prmtop file for both the PB calculation and for the non-polar calculation (see inp)
1: Use atom-type/charge-based radii by Tan and Luo for the PB calculation. Note that the radii are optimized for Amber atom types as in standard residues from the Amber database and should work fine for standard complexes such as protein-protein, protein-DNA. On the other hand, if a molecule in your system was built by antechamber, i.e., if GAFF atom types are used, or any other extrenal software, radii from the prmtop file should be used (radiopt = 0).
prbrad (Default = 1.4) Solvent probe radius (in Å). Allowed values are 1.4 and 1.6.
iprob (Default = 2.0) Mobile ion probe radius (in Å) for ion accessible surface used to define the Stern layer.
sasopt (Default = 0) Option to determine which kind of molecular surfaces to be used in the Poisson-Boltzmann implicit solvent model.
0: Use the solvent excluded surface as implemented by (ref.)
1: Use the solvent accessible surface. Apparently, this reduces to the van der Waals surface when the prbrad is set to zero.
2: Use the smooth surface defined by a revised density function. (ref.) This must be combined with `ipb > 2.
arcres (Default = 0.25) The arcres keyword gives the resolution (in Å) of dots used to represent solvent accessible arcs. More generally, arcres should be set to max(0.125 Å, 0.5h) (h is the grid spacing). (ref.)
memopt (Default = 0)
Option to turn the implicit membrane on and off. The membrane is implemented as a slab like region with a uniform or heterogeneous dielectric constant depth profile. Details of the implicit membrane setup can be found here.
0: No implicit membrane used.
1: Use a uniform membrane dielectric constant in a slab-like implicit membrane. (ref.)
2: Use a heterogeneous membrane dielectric constant in a slab-like implicit membrane. The dielectric constant varies with depth from a value of 1 in the membrane center to 80 at the membrane periphery. The dielectric constant depth profile was implemented using the PCHIP fitting. (ref.)
3: Use a heterogeneous membrane dielectric constant in a slab-like implicit membrane. The dielectric constant varies with depth from a value of 1 in the membrane center to 80 at the membrane periphery. The dielectric constant depth profile was implemented using the Spline fitting. (ref.)
mprob (Default = 2.70) Membrane probe radius (in Å). This is used to specify the highly different lipid molecule accessibility versus that of the water. (ref.)
mthick (Default = 40) Membrane thickness (in Å). This is different from the previous default of 20 Å.
mctrdz (Default = 0.0) Membrane center (in Å) in the z direction.
poretype (Default = 1) Turn on and off the automatic depth-first search method to identify the pore. (ref.)
0: Do not turn on the pore searching algorithm.
1: Turn on the pore searching algorithm.
npbopt (Default = 0) Option to select the linear, or the full nonlinear PB equation.
0: Linear PB equation (LPBE) is solved
1: Nonlinear PB equation (NLPBE) is solved
solvopt (Default = 1) Option to select iterative solvers.
1 Modified ICCG or Periodic (PICCG) if bcopt = 10.
2 Geometric multigrid. A four-level v-cycle implementation is applied by default.
3 Conjugate gradient (Periodic version available under bcopt = 10). This option requires a large linit to converge.
4 SOR. This option requires a large linit to converge.
5 Adaptive SOR. This is only compatible with npbopt = 1. This option requires a large linit converge. (ref.)
6 Damped SOR. This is only compatible with npbopt = 1. This option requires a large linit to converge. (ref.)
accept (Default = 0.001) Sets the iteration convergence criterion (relative to the initial residue).
linit (Default = 1000) Sets the maximum number of iterations for the finite difference solvers.
fillratio (Default = 4.0) The ratio between the longest dimension of the rectangular finite-difference grid and that of the solute. For macromolecules is fine to use 4, or a smaller value like 2. A default value of 4 is large enough to be used for a small solute, such as a ligand molecule. Using a smaller value for fillratio may cause part of the small solute to lie outside the finite-difference grid, causing the finite-difference solvers to fail.
scale (Default = 2.0)
Resolution of the Poisson Boltzmann grid. It is equal to the reciprocal of the grid spacing (space in pbsa).
nbuffer (Default = 0)
Sets how far away (in grid units) the boundary of the finite difference grid is away from the solute surface; i.e., automatically set to be at least a solvent probe or ion probe (diameter) away from the solute surface.New in v1.5.0
nfocus (Default = 2)
Set how many successive FD calculations will be used to perform an electrostatic focussing calculation on a molecule. When nfocus = 1, no focusing is used. It is recommended that nfocus = 1 when the multigrid solver is used.
fscale (Default = 8)
Set the ratio between the coarse and fine grid spacings in an electrostatic focussing calculation.New in v1.5.0
npbgrid (Default = 1)
Sets how often the finite-difference grid is regenerated.New in v1.5.0
bcopt (Default = 5)
Boundary condition options.
1: Boundary grid potentials are set as zero, i.e. conductor. Total electrostatic potentials and energy are computed.
5: Computation of boundary grid potentials using all grid charges. Total electrostatic potentials and energy are computed.
6: Computation of boundary grid potentials using all grid charges. Reaction field potentials and energy are computed with the charge singularity free formalism. (ref.)
10: Periodic boundary condition is used. Total electrostatic potentials and energy are computed. Can be used with solvopt = 1, 2, 3, or 4 and ipb = 1 or 2. It should only be used on charge-neutral systems. If the system net charge is detected to be nonzero, it will be neutralized by applying a small neutralizing charge on each grid (i.e. a uniform plasma) before solving.
eneopt (Default = 2) Option to compute total electrostatic energy and forces.
1: Compute total electrostatic energy and forces with the particle-particle particle-mesh (P3M) procedure outlined in Lu and Luo. (ref.) In doing so, energy term EPB in the output file is set to zero, while EEL includes both the reaction field energy and the Coulombic energy. The van der Waals energy is computed along with the particle-particle portion of the Coulombic energy. The electrostatic forces and dielectric boundary forces can also be computed. (ref.) This option requires a nonzero cutnb and bcopt = 5 for soluble proteins / bcopt = 10 for membrane proteins.
2: Use dielectric boundary surface charges to compute the reaction field energy. Both the Coulombic energy and the van der Waals energy are computed via summation of pairwise atomic interactions. Energy term EPB in the output file is the reaction field energy. EEL is the Coulombic energy.
3: Similar to the first option above, a P3M procedure is applied for both solvation and Coulombic energy and forces for larger systems.
4: Similar to the third option above, a P3M procedure for the full nonlinear PB equation is applied for both solvation and Coulombic energy and forces for larger systems. A more robust and clean set of routines were used for the P3M and dielectric surface force calculations.
frcopt (Default = 0) Option to compute and output electrostatic forces to a file named force.dat in the working directory.
0: Do not compute or output atomic and total electrostatic forces.
1: Reaction field forces are computed by trilinear interpolation. Dielectric boundary forces are computed using the electric field on dielectric boundary. The forces are output in the unit of kcal/mol·Å.
2: Use dielectric boundary surface polarized charges to compute the reaction field forces and dielectric boundary forces (ref.) The forces are output in the unit of kcal/mol·Å.
3: Reaction field forces are computed using dielectric boundary polarized charge. Dielectric boundary forces are computed using the electric field on dielectric boundary. (ref.) The forces are output in kcal/mol·Å.
scalec (Default = 0) Option to compute reaction field energy and forces.
0: Do not scale dielectric boundary surface charges before computing reaction field energy and forces.
1: Scale dielectric boundary surface charges using Gauss’s law before computing reaction field energy and forces.
cutfd (Default = 5.0)
Atom-based cutoff distance to remove short-range finite-difference interactions, and to add pairwise charge-based interactions. This is used for both energy and force calculations. See Eqn (20) in Lu and Luo. (ref.)
cutnb (Default = 0.0)
Atom-based cutoff distance for van der Waals interactions, and pairwise Coulombic interactions when eneopt = 2. When cutnb is set to the default value of 0, no cutoff will be used for van der Waals and Coulombic interactions, i.e., all pairwise interactions will be included. When eneopt = 1, this is the cutoff distance used for van der Waals interactions only. The particle-particle portion of the Coulombic interactions is computed with the cutoff of cutfd.
nsnba (Default = 1)
Sets how often (steps) atom-based pairlist is generated.
decompopt (Default = 2)
Option to select different decomposition schemes when inp = 2. See (ref.) for a detailed discussion of the different schemes. The σ decomposition scheme is the best of the three schemes studied. (ref.) As discussed in (ref.), decompopt = 1 is not a very accurate approach even if it is more straightforward to understand the decomposition.1: The 6/12 decomposition scheme.2: The σ decomposition scheme.3: The WCA decomposition scheme.
use_rmin (Default = 1)
The option to set up van der Waals radii. The default is to use van der Waals rmin to improve the agreement with TIP3P.
sprob (Default = 0.557)
Solvent probe radius (in Å) for solvent accessible surface area (SASA) used to compute the dispersion term, default to 0.557 Å in the σ decomposition scheme as optimized in (ref.) with respect to the TIP3P solvent and the PME treatment. Recommended values for other decomposition schemes can be found in Table 4 of (ref.). If use_sav = 0 (see below), sprob can be used to compute SASA for the cavity term as well. Unfortunately, the recommended value is different from that used in the dispersion term calculation as documented in (ref.). Thus, two separate calculations are needed when use_sav = 0, one for the dispersion term and one for the cavity term. Therefore, please carefully read (ref.) before proceeding with the option of use_sav = 0. Note that sprob was used for ALL three terms of solvation free energies, i.e., electrostatic, attractive, and repulsive terms in previous releases in Amber. However, it was found in the more recent study (ref.) that it was impossible to use the same probe radii for all three terms after each term was calibrated and validated with respect to the TIP3P solvent. (ref.)
vprob (Default = 1.300)
Solvent probe radius (in Å) for molecular volume (the volume enclosed by SASA) used to compute non-polar cavity solvation free energy, default to 1.300 Å, the value optimized in (ref.) with respect to the TIP3P solvent. Recommended values for other decomposition schemes can be found in Tables 1-3 of (ref.).
rhow_effect (Default = 1.129)
Effective water density used in the non-polar dispersion term calculation, default to 1.129 for decompopt = 2, the σ scheme. This was optimized in (ref.) with respect to the TIP3P solvent in PME. Optimized values for other decomposition schemes can be found in Table 4 of (ref.).
use_sav (Default = 1)
The option to use molecular volume (the volume enclosed by SASA) or to use molecular surface (SASA) for cavity term calculation. Recent study shows that the molecular volume approach transfers better from small training molecules to biomacromolecules.0: Use SASA to estimate cavity free energy1: Use the molecular volume enclosed by SASANew in v1.5.0
cavity_surften (Default = 0.0378)
The regression coefficient for the linear relation between the total non-polar solvation free energy (inp = 1), or the cavity free energy (inp = 2) and SASA/volume enclosed by SASA. The default value is for inp = 2 and set to the best of three tested schemes as reported in (ref.), i.e.decompopt = 2, use_rmin = 1, and use_sav = 1. See recommended values in Tables 1-3 for other schemes.
cavity_offset (Default = -0.5692)
The regression offset for the linear relation between the total non-polar solvation free energy (inp= 1), or the cavity free energy (inp = 2) and SASA/volume enclosed by SASA. The default value is for inp = 2 and set to the best of three tested schemes as reported in (ref.), i.e.decompopt = 2, use_rmin = 1, and use_sav = 1. See recommended values in Tables 1-3 for other schemes.
maxsph (Default = 400)
Approximate number of dots to represent the maximum atomic solvent accessible surface. These dots are first checked against covalently bonded atoms to see whether any of the dots are buried. The exposed dots from the first step are then checked against a non-bonded pair list with a cutoff distance of 9 Å to see whether any of the exposed dots from the first step are buried. The exposed dots of each atom after the second step then represent the solvent accessible portion of the atom and are used to compute the SASA of the atom. The molecular SASA is simply a summation of the atomic SASA’s. A molecular SASA is used for both PB dielectric map assignment and for NP calculations.New in v1.5.0
maxarcdot (Default = 1500)
Number of dots used to store arc dots per atom.
npbverb (Default = 0)
Verbose mode.0: Off1: OnNew in v1.5.0
&rism
closure (Default = "kh")
Comma separate list of closure approximations. If more than one closure is provided, the 3D-RISM solver will use the closures in order to obtain a solution for the last closure in the list when no previous solutions are available. The solution for the last closure in the list is used for all output. The use of several closures combined with different tolerances can be useful to overcome convergence issues (see §7.3.1)
gfcorrection (Default = 0)
Compute the Gaussian fluctuation excess chemical potential functional.
0: Off
1: On
pcpluscorrection (Default = 0)
Compute the PC+/3D-RISM excess chemical potential functional.
0: Off
1: On
noasympcorr (Default = 1)
Use long-range asymptotic corrections for thermodynamic calculations.0: Do not use long-range corrections1: Use the long-range correctionsNew in v1.5.0
treeDCF (Default = 1)
Use direct sum, or the treecode approximation to calculate the direct correlation function long-range asymptotic correction.0: Use direct sum1: Use treecode approximationNew in v1.5.0
treeTCF (Default = 1)
Use direct sum, or the treecode approximation to calculate the total correlation function long-range asymptotic correction.0: Use direct sum1: Use treecode approximationNew in v1.5.0
treeCoulomb (Default = 1)
Use direct sum, or the treecode approximation to calculate the Coulomb potential energy.0: Use direct sum1: Use treecode approximationNew in v1.5.0
treeDCFMAC (Default = 0.1)
Treecode multipole acceptance criterion for the direct correlation function long-range asymptotic correction.New in v1.5.0
treeTCFMAC (Default = 0.1)
Treecode multipole acceptance criterion for the total correlation function long-range asymptotic correction.New in v1.5.0
treeCoulombMAC (Default = 0.1)
Treecode multipole acceptance criterion for the Coulomb potential energy.New in v1.5.0
treeDCFOrder (Default = 2)
Treecode Taylor series order for the direct correlation function long-range asymptotic correction.New in v1.5.0
treeTCFOrder (Default = 2)
Treecode Taylor series order for the total correlation function long-range asymptotic correction. Note that the Taylor expansion used does not converge exactly to the TCF long-range asymptotic correction, so a very high order will not necessarily increase accuracy.New in v1.5.0
treeCoulombOrder (Default = 2)
Treecode Taylor series order for the Coulomb potential energy.New in v1.5.0
treeDCFN0 (Default = 500)
Maximum number of grid points contained within the treecode leaf clusters for the direct correlation function long-range asymptotic correction. This sets the depth of the hierarchical octtree.New in v1.5.0
treeTCFN0 (Default = 500)
Maximum number of grid points contained within the treecode leaf clusters for the total correlation function long-range asymptotic correction. This sets the depth of the hierarchical octtree.New in v1.5.0
treeCoulombN0 (Default = 500)
Maximum number of grid points contained within the treecode leaf clusters for the Coulomb potential energy. This sets the depth of the hierarchical octtree.New in v1.5.0
buffer (Default = 14)
Minimum distance (in Å) between solute and edge of solvation box. Specify this with grdspc below. Mutually exclusive with ng and solvbox. See §7.2.3 for details on how this affects numerical accuracy and how this interacts with ljTolerance, and tolerancewhen < 0: Use fixed box size (see ng and solvbox below)when >= 0: Use buffer distance
grdspc(Default = 0.5,0.5,0.5)
Grid spacing (in Å) of the solvation box. Specify this with buffer above. Mutually exclusive with ng and solvbox.
ng (Default = -1,-1,-1)
Comma separated number of grid points to use in the x, y, and z directions. Used only if buffer < 0. Mutually exclusive with buffer and grdspc above, and paired with solvbox below.
solvbox (Default = -1,-1,-1)
Sets the size in Å of the fixed size solvation box. Used only if buffer < 0. Mutually exclusive with buffer and grdspc above, and paired with ng above.
solvcut (Default = 14)
Cutoff used for solute-solvent interactions. The default value is that of buffer. Therefore, if you set buffer < 0 and specify ng and solvbox instead, you must set solvcut to a nonzero value; otherwise the program will quit in error.
tolerance (Default = 0.00001)
A comma-separated list of maximum residual values for solution convergence. This has a strong effect on the cost of 3D-RISM calculations (smaller value for tolerance -> more computation). When used in combination with a list of closures it is possible to define different tolerances for each of the closures. This can be useful for difficult to converge calculations (see §7.4.1). For the sake of efficiency, it is best to use as high a tolerance as possible for all but the last closure. See §7.2.3 for details on how this affects numerical accuracy and how this interacts with ljTolerance, buffer, and solvbox.
ljTolerance (Default = -1)
Lennard-Jones accuracy (Optional.) Determines the Lennard-Jones cutoff distance based on the desired accuracy of the calculation. See §7.2.3 for details on how this affects numerical accuracy and how this interacts with tolerance, buffer, and solvbox.
asympKSpaceTolerance (Default = -1)
Tolerance reciprocal space long range asymptotics accuracy (Optional.) Determines the reciprocal space long range asymptotic cutoff distance based on the desired accuracy of the calculation. See §7.2.3 for details on how this affects numerical accuracy. Possible values are:when < 0: asympKSpaceTolerance = tolerance/10when = 0: no cutoffwhen > 0: given value determines the maximum error in the reciprocal-space long range asymptotics calculations
mdiis_del (Default = 0.7)
MDIIS step size.New in v1.5.0
mdiis_nvec (Default = 5)
Number of previous iterations MDIIS uses to predict a new solution.New in v1.5.0
mdiis_restart (Default = 10)
If the current residual is mdiis_restart times larger than the smallest residual in memory, then the MDIIS procedure is restarted using the lowest residual solution stored in memory. Increasing this number can sometimes help convergence.New in v1.5.0
maxstep (Default = 10000)
Maximum number of iterations allowed to converge on a solution.New in v1.5.0
npropagate (Default = 5)
Number of previous solutions propagated forward to create an initial guess for this solute atom configuration.=0: Do not use any previous solutions= 1..5: Values greater than 0 but less than 4 or 5 will use less system memory but may introduce artifacts to the solution (e.g., energy drift).New in v1.5.0
polardecomp (Default = 0)
Decomposes solvation free energy into polar and non-polar components. Note that this typically requires 80% more computation time.
0: Don’t decompose solvation free energy into polar and non-polar components.
1: Decompose solvation free energy into polar and non-polar components.
entropicdecomp (Default = 0)
Decomposes solvation free energy into energy and entropy components. Also performs temperature derivatives of other calculated quantities. Note that this typically requires 80% more computation time and requires a .xvv file version 1.000 or higher (available within GMXMMPBSA data folder).
0: No entropic decomposition
1: Entropic decomposition
rism_verbose (Default = 0)
Level of output in temporary RISM output files. May be helpful for debugging or following convergence.0: just print the final result1: additionally prints the total number of iterations for each solution2: additionally prints the residual for each iteration and details of the MDIIS solver (useful for debugging and convergence analyses)
&alanine_scanning
mutant_res (Default = None. Must be defined)
Define the specific residue that is going to be mutated. Use the following format CHAIN/RESNUM (e.g.: 'A/350') or CHAIN/RESNUM:INSERTION_CODE if applicable (e.g.: "A/27:B").
mutant (Default = "ALA")
Defines the residue that it is going to be mutated for.
Allowed values are:
"ALA" or "A": Alanine scanning
"GLY" or "G": Glycine scanning
mutant_only (Default = 0)
Option to perform specified calculations only for the mutants.
0: Perform calcultion on mutant and original
1: Perform calcultion on mutant only
cas_intdiel (Default = 0)
The dielectric constant (intdiel(GB)/indi(PB)) will be modified depending on the nature of the residue to be mutated.
0: Don’t
1: Adaptative intdiel assignation
intdiel_nonpolar (Default = 1)
Define the intdiel(GB)/indi(PB) value for non-polar residues (PHE, TRP, VAL, ILE, LEU, MET, PRO, CYX, ALA, GLY, PRO)
intdiel_polar (Default = 3)
Define the intdiel(GB)/indi(PB) value for polar residues (TYR, SER, THR, CYM, CYS, HIE, HID, ASN, GLN, ASH, GLH, LYN)
intdiel_positive (Default = 5)
Define the intdiel(GB)/indi(PB) value for positive charged residues (LYS, ARG, HIP)
intdiel_negative (Default = 5)
Define the intdiel(GB)/indi(PB) value for negative charged residues (GLU, ASP)
&decomp
idecomp
Energy decomposition scheme to use:
1: Per-residue decomp with 1-4 terms added to internal potential terms
2: Per-residue decomp with 1-4 EEL added to EEL and 1-4 VDW added to VDW potential terms
3: Pairwise decomp with 1-4 terms added to internal potential terms
4: Pairwise decomp with 1-4 EEL added to EEL and 1-4 VDW added to VDW potential terms
dec_verbose (Default = 0)
Set the level of output to print in the decomp_output file.
0: DELTA energy, total contribution only
1: DELTA energy, total, sidechain, and backbone contributions
2: Complex, Receptor, Ligand, and DELTA energies, total contribution only
3: Complex, Receptor, Ligand, and DELTA energies, total, sidechain, and backbone contributions
print_res (Default = "within 6")
Select residues whose information is going to be printed in the output file. The default selection should be sufficient in most cases, however we have added several additional notations
csv_format (Default = 1)
Print the decomposition output in a Comma-Separated-Values (CSV) file. CSV files open natively in most spreadsheets.
0: data to be written out in the standard ASCII format.
1: data to be written out in a CSV file, and standard error of the mean will be calculated and included for all data.
&nmode
nmstartframe
Frame number to begin performing nmode calculations on
nmendframe(Default = 1000000)
Frame number to stop performing nmode calculations on
nminterval(Default = 1)
Offset from which to choose frames to perform nmode calculations on
nmode_igb (Default = 1)
Value for Generalized Born model to be used in calculations. Options are:0: Vacuum1: HCT GB model
nmode_istrng (Default = 0.0)
Ionic strength to use in nmode calculations. Units are Molarity (M). Non-zero values are ignored if nmode_igb is 0 above.
dielc (Default = 1.0)
Distance-dependent dielectric constant
drms (Default = 0.001)
Convergence criteria for minimized energy gradient.
maxcyc (Default = 10000)
Maximum number of minimization cycles to use per snapshot in sander.
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