VMD-L Mailing List

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Thu Apr 06 2006 - 13:18:34 CDT

Dear John and Marcos,

Thank you for the email. I looked up definitions for NTER and CTER
and their chemical structures; this is probably not what I'd expect
in my simulations.
I wonder if there are options for "capped"
termini, ie Acetyl and N-methyl options, such that charges at termini
are neutral. Or is there another way to get around
  with charges at ends,
please drop a hint.

Thank you!
Sincerely,
Margaret

On Thu, 6 Apr 2006, Marcos Sotomayor wrote:

>
> 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
>> Beckman Institute for Advanced Science and Technology
>> 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
>>
>

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
------------------------------------------------------------