On 16/06/2011 11:01 PM, maria goranovic wrote:
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
Rename all the HISB residues in your input coordinate file to whatever
OPLS/AA wants.
Mark
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