VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Mar 02 2011 - 23:48:24 CST

Assuming you're using the latest version of VMD with support for patches in Mutator (if the plugin says it does not support patches, then it's an old version), make sure that it can find the topology files exactly where the psf says they are (keeping mind the paths you have are relative). If it can't, it will just take a default topology file which will not have your HRCY patch.

On Mar 2, 2011, at 3:27 PM, Thomas Freeman wrote:

> Hello all,
>
> I am working on trying to mutate a residue on cytochrome c using the VMD
> mutator plugin. Doing this however, as the help mentions, causes a loss
> of the patches used to attach the heme to the protein. I read that
> patches can be applied by adding the patch command to the REMARKS
> section of the psf file, however, even with the following remarks in my
> psf file I still lose the connections of the protein to the heme:
>
> REMARKS original generated structure x-plor psf file
> REMARKS 3 patches were applied to the molecule.
> REMARKS topology toppar/top_c_heme.inp
> REMARKS topology toppar/top_all22_prot.inp
> REMARKS segment PROT { first GLYP; last CTER; auto angles dihedrals }
> REMARKS segment HEC { first NONE; last NONE; auto angles dihedrals }
> REMARKS defaultpatch GLYP PROT:1
> REMARKS defaultpatch CTER PROT:104
> REMARKS patch HRCY PROT:14 PROT:17 PROT:18 PROT:80 HEC:105
>
> Thanks in advance,
>
> --
> Thomas Freeman
> Graduate Student
> Chemistry 67 Teaching Assistant
> Pletneva Research Group
> Department of Chemistry
> Dartmouth College