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粗粒化-- Martini-- ‘[moleculetype]‘ Invalid order for directive moleculetype

戚高洁
2023-12-01
[user@localhost bilayer-lipidome]$ gmx grompp -f minimization.mdp -c 128_noW.gro -p dppc.top -o dppc-min-init.tpr
                      :-) GROMACS - gmx grompp, 2021.1 (-:

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GROMACS:      gmx grompp, version 2021.1
Executable:   /usr/local/gromacs/bin/gmx
Data prefix:  /usr/local/gromacs
Working dir:  /home/user/MD/Martini/bilayer-lipidome

Command line:
  gmx grompp -f minimization.mdp -c 128_noW.gro -p dppc.top -o dppc-min-init.tpr

Ignoring obsolete mdp entry 'ns_type'
Setting the LD random seed to 2146394111

-------------------------------------------------------
Program:     gmx grompp, version 2021.1
Source file: src/gromacs/gmxpreprocess/topio.cpp (line 556)

Fatal error:
Syntax error - File martini_v2.0_DPPC_01.itp, line 26
Last line read:
'[moleculetype]'
Invalid order for directive moleculetype

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------

查看top文件:

#include "martini_v2.0_DPPC_01.itp"
#include "martini_v2.1.itp"

[ system ]
DPPC BILAYER SELF-ASSEMBLY

[ molecules ]
DPPC 128

martini_v2.1.itp定义粒子类型,martini_v2.0_DPPC_01.itp只定义DPPC
top文件修改成下面,就可成功运行:


#include "martini_v2.1.itp"
#include "martini_v2.0_DPPC_01.itp"

[ system ]
DPPC BILAYER SELF-ASSEMBLY

[ molecules ]
DPPC 128
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