On 10/17/12 9:41 AM, spin wrote:
Thank you, Peter.
Do you mean that the [atomtypes] section is not important? In other words,
Gromacs will skip them if the data have been given in [pairtypes] section,
isn't it? I have type the follow command:
/pdb2gmx -f *.pdb -o *.gro -p *.top -ss -his
grompp -v -f vac-min.mdp -c *.gro -p *.top -o vac-min.tpr/
The first are successful, but the second failed. The error information is :
/Fatal error:
Atomtype CG301 not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors/
I tried to add the CG301 to [atomtypes], and typed the command again, but it
gave me next atomtype XX not found. It seems that I have to add all CGenFF
atomtypes manually.
I thought that it is due to the absence of atomtypes information. Because
David's script did not give me the atomtypes information. I don't know why
it was.
I tried to add the CG301 to [atomtypes], and typed the command again, but it
gave me next atomtype XX not found. It seems that I have to add all CGenFF
atomtypes manually.
Any atom type that is not already incorporated into the parent force field (i.e.
CHARMM27 in Gromacs) must be added manually to an [atomtypes] directive either
in the .top (prior to [moleculetype] declaration) or in ffnonbonded.itp in the
force field directory.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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