[gmx-users] Re: The problem of converting CGenff parameters to those of Gromacs

[Justin Lemkul]

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

========================================