[gmx-users] Re: Interchain Disulfide Bond

[jneeraj]

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 ?

Thanks
neeraj

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