VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Sep 15 2006 - 19:41:23 CDT

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