[gmx-users] BHIS for HIS?
tsjerkw at gmail.com
Wed Apr 11 06:39:44 CEST 2007
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
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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