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

[maria goranovic]

thought of that, but the trajectory also has HISB data .. so I guess I will
have to alter it frame by frame ?

On Thu, Jun 16, 2011 at 4:32 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

> 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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-- 
Maria G.
Technical University of Denmark
Copenhagen
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