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

[Mark Abraham]

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