VMD-L Mailing List

From: Margaret S. Cheung (mscheung_at_uh.edu)
Date: Fri Sep 15 2006 - 20:08:41 CDT

Thank you for the pointers. I'd like to try these programs out.
Thanks.
Margaret

Peter Freddolino wrote:
> To expand a bit on that, you're much more likely to get a good result if
> you use a program like rosetta or modeller to build the complete
> structure, since they're designed to optimize the contacts in such cases.
> Peter
>
> JC Gumbart wrote:
>
>> Well, Psfgen can always guess any number of missing atoms for a residue
>> as long as it has at least one based on what is in the topology file.
>> This is not to say it would be a good guess of course.
>>
>> For missing residues, you would have to guess at least one atom per
>> residue for it to fill them in.
>>
>> Would this be sufficient for your needs?
>>
>> On Sep 15, 2006, at 11:38 AM, Margaret Shun Cheung wrote:
>>
>>
>>> Dear All,
>>>
>>> I have a low resolution data that only have a few atoms available for
>>> each amino acids in a protein. I'd like to build a full atomistic
>>> protein based on these known info as constraints.
>>> Did anyone how to do this? It's kinda irrelavent to VMD, but I figured
>>> given a large set of experts here, somebody probably will have an
>>> answer to this.
>>> Thanks.
>>>
>>> Margaret S. Cheung,
>>> ============================================================
>>> Assistant Professor 629C Science and Research I Department of Physics
>>> University of Houston http://thoth.phys.uh.edu/~mscheung
>>> Houston, TX 77204 email: mscheung_at_uh.edu
>>> ------------------------------------------------------------
>>> contact info until January 2007
>>> Room 2112 Tel: (301) 405-9307
>>> 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
Assistant Professor
Department of Physics
629C Science and Research 1
University of Houston
Houston, TX 77204-5005
email:   mscheung_at_uh.edu
website: http://thoth.phys.uh.edu/~mscheung/