Re: Interactive protonation

From: Giacomo Fiorin (
Date: Sat Mar 28 2009 - 18:48:43 CDT

Hi Dimitry, what you're looking for is the "patch" command in the
input for psfgen. If you're using the graphical front-end AutoPSF
inside VMD, you can even select them from a pull-down menu.


---- -----
 Giacomo Fiorin
   Center for Molecular Modeling at
     University of Pennsylvania
     231 S 34th Street, Philadelphia, PA 19104-6323
 phone: (+1)-215-573-4773
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 mail: giacomo.fiorin_<at>
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On Sat, Mar 28, 2009 at 5:46 PM, DimitryASuplatov <> wrote:
> Hello,
> 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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