Hi,
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.
Cheers,
Erik
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.
Cheers,
Tsjerk
On 4/11/07, Rongliang Wu <[EMAIL PROTECTED]> wrote:
hello,gmx-users，
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
[EMAIL PROTECTED]
2007-04-11
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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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