[gmx-users] BHIS for HIS?
lindahl at cbr.su.se
Wed Apr 11 08:32:11 CEST 2007
pdb2gmx tries to choose the HIS protonation based on hydrogen bond
patterns in the structure, so unless you are absolutely certain you
need the alternative state you should need to do anything. In the
latter case, just edit the name in the PDB file (to HISB or HISH)
prior to running pdb2gmx.
On Apr 11, 2007, at 6:39 AM, Tsjerk Wassenaar wrote:
> Hi Rongliang Wu,
> You could try to get your hands on a GROMOS manual... Alternatively,
> draw the histidines using the information in the rtp files.
> Alternatively, take a histidine, run it through pdb2gmx with -his and
> try all options. Histidine has different protonation states, and one
> of the histidines is the one bound to heme iron.
> On 4/11/07, Rongliang Wu <wurl04 at iccas.ac.cn> wrote:
>> i am trying to simulate a peptide with residue HIS, the
>> default in pdb2gmx used HISB for HIS in both oplsaa and gromos96
>> force field, but i found there are HIS1,HISH,HISB etc in the rtp
>> files, i am not sure whether HISB will suffice for my system, i
>> intend to simulate the binding of surfactants with the peptide.
>> what are the difference?
>> is there anywhere i can find the detailed description for
>> these residues?
>> Rongliang Wu
>> wurl04 at iccas.ac.cn
>> gmx-users mailing list gmx-users at gromacs.org
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> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
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