Steven Neumann wrote:
Dear Gmx Users,
Does anyone know why in Charmm27 ff under Gromacs the residue HIS is
taken as residue HSE from rtp file and written as NONcharged?
pdb2gmx decides the protonation state to assign based on a hydrogen bond network
search. This is true for all force fields. If you are unsatisfied with the
chosen protonation, there are command line options to interactively change the
protonation state of any titratable residues.
-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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