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9 years 5 months ago #4168 by doa.hawamdeh
GROMACS was created by doa.hawamdeh
Hello,

I am beginner in using GROMACS in MD simulation for PAMAM dendrimer (MARTINI Force field). I would like to ask how can I get the topology file? I have *.itp file and I tried to write the topology file but when I commanded ( grompp -v -f minim.mdp -c g4.gro -p g4.top -o g4-EM-vacuum.tpr) to minimizing the system in vacuum, I got (Fatal error:
Syntax error - File g4.itp, line 1
Last line read:
'[ moleculetype ]'
Invalid order for directive moleculetype )??

Please could anyone help me?

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9 years 4 months ago #4169 by xavier
Replied by xavier on topic GROMACS
The error message tells that there is a problem in the formatting of your topology.

Use an existing topology to check where the mistake can be. You'll find plenty on the website.

doa.hawamdeh wrote: Hello,

I am beginner in using GROMACS in MD simulation for PAMAM dendrimer (MARTINI Force field). I would like to ask how can I get the topology file? I have *.itp file and I tried to write the topology file but when I commanded ( grompp -v -f minim.mdp -c g4.gro -p g4.top -o g4-EM-vacuum.tpr) to minimizing the system in vacuum, I got (Fatal error:
Syntax error - File g4.itp, line 1
Last line read:
'[ moleculetype ]'
Invalid order for directive moleculetype )??

Please could anyone help me?

Please Log in or Create an account to join the conversation.

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