VMD-L Mailing List

From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Thu Apr 06 2006 - 00:02:47 CDT

Hi Margaret,

psfgen will build segments of your protein using a topology file which
defines different residues and patches. The usual CHARMM topology file
assumes standard protonation states for residues labeled ASP (-), GLU (-),
ARG (+), and LYS (+). There are three options for histidine and you
need to choose one of them (HSE, HSD or HSP, you may want to see the
first chapter of the NAMD tutorial). There are several options for the
termini too (charged and uncharged, etc.), which can be selected through
patches (which can also be used to protonate ASP and GLU, see the
patches PRES ACP, CTER, CT1, ASPP and GLUP in the CHARMM topology file
provided by VMD).

hope that helps!
Marcos

On Wed, 5 Apr 2006, John Stone wrote:

> Hi,
> You'll want to read through the NAMD tutorial section
> about topology files, as it describes the purpose of patches
> for the the terminal residues:
> http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-html/node21.html
>
> I don't know the answer regarding charged states, you'll have to ask
> Jim Phillips about that, (jim_at_ks.uiuc.edu) as he wrote the psfgen.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Apr 04, 2006 at 05:23:25PM -0400, Margaret Shun Cheung wrote:
>> Dear VMD wizards,
>>
>> I would like to know what kind of charged states psfgen would generate
>> from a standard pdb structure.
>> Do I have to worry about adding charges at all?
>> Also, when I read the psfgen user guide, it said psfgen will
>> patch N-terminal and C-terminal atoms. What does "patch" means? Do these
>> termini carry charges?
>> Thank you.
>> Sincerely,
>> Margaret S. Cheung,
>> Ph. D. Postdoctoral Fellow,
>>
>> ------------------------------------------------------------
>> Room 2117 Tel: (301) 405-4892
>> Inst. for Phys. Sci. & Tech. Fax: (301) 314-9404
>> University of Maryland http://glue.umd.edu/~mscheung
>> College Park, MD 20742-2431 email: mscheung_at_ipst.umd.edu
>> ------------------------------------------------------------
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
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> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>