[gmx-users] Re: Interchain Disulfide Bond

[Mark Abraham]

On 21/02/2012 12:33 PM, jneeraj wrote:
> Thank you Mark for you prompt response. I tried:
>
> $pdb2gmx -ignh -merge all -chainsep ter -ff amber99sb -water tip3p -f<pdb>
> -o<gro>  -p<top>
> $grompp -f<mdp>  -c<gro>  -p<top>  -o<tpr>
>
> and it works perfectly, i.e. it correctly creates interchain disulfide bond.
>
> However, when I use charmm27 force field instead of amber99sb, I get the
> following error from grompp:
> ----------------------------------------------------------------------------
> Program grompp, VERSION 4.5.5
> Source code file: toppush.c, line: 1346
>
> Fatal error:
> Unknown cmap torsion between atoms 3224 3226 3228 3234 3237
> ----------------------------------------------------------------------------
>
> So I believe this error is specific to charmm27 force-field. Any thoughts ?

Because those are the atoms across the 1-C 2-N region, that suggests 
that the mechanism that adds CMAP to the backbone is not interacting 
correctly with the -merge mechanism. Please open a new issue on Redmine 
http://redmine.gromacs.org <http://redmine.gromacs.org/> and attach 
files that will reproduce the problem. If my guess is correct, the fix 
should be straightforward.

Mark
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