From: Giacomo Fiorin (gfiorin_at_seas.upenn.edu)
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
---- -----
Giacomo Fiorin
Center for Molecular Modeling at
University of Pennsylvania
231 S 34th Street, Philadelphia, PA 19104-6323
phone: (+1)-215-573-4773
fax: (+1)-215-573-6233
mobile: (+1)-267-324-7676
mail: giacomo.fiorin_<at>_gmail.com
web: http://www.cmm.upenn.edu/
---- ----
On Sat, Mar 28, 2009 at 5:46 PM, DimitryASuplatov <genesup_at_gmail.com> 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.
> SDA
>
>
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