VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Sep 15 2006 - 20:06:54 CDT

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
>> ============================================================