Interactive protonation

From: DimitryASuplatov (
Date: Sat Mar 28 2009 - 16:46:51 CDT


how can I choose the protonation state of his, lys, asp, glu and
terminal groups in namd when building psf? I am especially interested
in choosing protonation states of cooh and nh3 groups of n- and
c-terminal residues.
I am new to namd and I was using gromacs previously. In gromacs this
is done explicitly with pdb2gmx program and appropriate flags -his,
-asp, -glu, -ter etc.

Thanks, I appreciate your time.

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