Re: Interactive protonation

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sat Mar 28 2009 - 19:26:51 CDT

Just to elaborate on what Giacomo said, as you'll note in the structure
building portion of the NAMD tutorial you can define both terminal
patches for each chain, and patches on a residue by residue basis for
further modifications. You can find the available patches by looking at
the topology file. For example, NTER gives a protonated N terminus, ACE
gives an N-acetyl blocked N terminus, ASPP gives a protonated aspartic
acid residue, and so on.

Peter

Giacomo Fiorin wrote:
> 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
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> 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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