changing protonation states for a pdb with more than a single polypeptide

From: Elia Zomot (
Date: Tue May 12 2009 - 18:47:41 CDT

Dear all,

The pdb file I'm working on is a protein dimer, embedded in a bilipid
membrane with water molecules.
Applying the (de)protonation patches to the "raw" monomer alone works fine.
However, when I try to apply them to the pdb file of the dimer+lipid+water I
get screwed up results (irregularities in the shape of the protein, very
long bonds, just a single monomer instead of the dimer, etc.)
I assume the problem is likely bec of the "segment" command (script I used
below) I am using which will have to be redefined to include two segments
for the two subunits (A and B) and other segments for the lipids and water
Any ideas on how to do that assuming that is the problem?

Thanks in advance

package require psfgen
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSD # HSD and not HSE so as to be able to apply the
HS2 patch afterwards
pdbalias atom ILE CD1 CD
pdbalias atom NA SOD
pdbalias atom CL CLA
segment U {pdb filename.pdb}
patch HS2 U:7 U:377 U:480
patch GLUP U:112 U:287 U:419
coordpdb filename.pdb U
writepdb new_filename.pdb
writepsf new_filename.psf

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