Acoot Brett wrote:
Dear All,
For low resolution structure PDB, the protonation state of histidine is
niot clear. Then how does pdb2gmx treat the protonation state of HS?
Even for high resolution structure of protein, the protonation state of
HIS is usallly unclear or unspefified.
In the manual og gromacs, although it involves different protonation
state of HIS (and some other residues), but the whole manual never
request us to modify the PDB file for pdb2gmx input.
Thus can we consider pdb2gmx process the protonation state of residues
(including HIS) automatically?
I answered this yesterday:
http://lists.gromacs.org/pipermail/gmx-users/2012-April/070129.html
Please pay attention to advice you've already been given, or else people become
less likely to give it.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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