VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Apr 06 2006 - 13:34:49 CDT

Dear Margaret,
you may want to look at some of the other patches that Marcos mentioned
in his email, such as ACE (acetylated N terminus) or CT1 (methylated C
terminus). They are all present in the topology file.
Best,
Peter

Margaret Shun Cheung wrote:

> 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
> ------------------------------------------------------------