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GROMACS
- doa.hawamdeh
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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?
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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- xavier
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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.
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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