[gmx-users] residue HISB not found 4.5.3 versus 4.0.7 OPLSAA

[maria goranovic]

Hi

I had a simulation run with 4.0.7, using opls-aa for a protein in water.

I now use part of the protein coordinates output from the simulation, and
use pdb2gmx as:

pdb2gmx -f conf.gro -ff oplsaa -ignh

pdb2gmx complains that it cannot find HISB. I checked that the topology
files in 4.5.3 do not contain HISB, while those in 4.0.7 do.

It does not suffice to create another copy of the HISE topology in the .rtp
file and call it HISB, because a number of hydrogen atoms also have been
renamed?

What can be done? I want to use 4.5.3 because I would prefer to retain
residue numbering

Maria


-- 
Maria G.
Technical University of Denmark
Copenhagen
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110616/fffbcd52/attachment.html>