VMD-L Mailing List

From: Thomas Freeman (Thomas.L.Freeman_at_dartmouth.edu)
Date: Wed Mar 02 2011 - 15:27:21 CST

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