VMD-L Mailing List

From: Margaret Shun Cheung (mscheung_at_ipst.umd.edu)
Date: Thu Apr 06 2006 - 13:45:26 CDT

Dear All,
Thank you very much for the tips!
Sincerely,
Margaret

On Thu, 6 Apr 2006, Peter Freddolino wrote:

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

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
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