VMD-L Mailing List

From: Leonardo G. Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Wed Jun 14 2006 - 13:09:36 CDT

On Wed, Jun 14, 2006 at 04:43:20PM +0530, Moumita Maiti wrote:
> Hi,
>
> I am trying to generate a psf file which contains nine segments,
> where two of them are DNA. I tried to
> run psfgen through vmd, then I get the following warnings,
>
> Can anybody help me so that I can get rid of these warnings?
>
> Info: generating structure...
> Info: skipping conformation O3'-O5'-P-O2P at beginning of segment.
> Info: skipping conformation O3'-O5'-P-O1P at beginning of segment.
> Info: skipping conformation O3'-P-O5'-C5' at beginning of segment.
> Info: skipping bond O3'-P at end of segment.
> Info: skipping conformation C3'-O3'-P-O5' at end of segment.
> Info: skipping conformation C4'-C3'-O3'-P at end of segment.
> no atom C in residue THY:-72 of segment DN0
> Warning: add conformation failed in patch NTER
> no atom CA in residue THY:73 of segment DN0
> Warning: add improper failed in patch CTER
> no atom CA in residue THY:73 of segment DN0
> Warning: add conformation failed in patch CTER
> no atom N in residue THY:73 of segment DN0
> Warning: add conformation failed in patch CTER

It looks like you are trying to apply the patches NTER and CTER to your
DNA segment, but they are protein terminii. Please take a look at the
patches 5PHO, 5TER, 3PHO, and 3TER in the topology file. You probably
want to apply 5PHO and 3TER to your DNA segments. It's also worthy
looking at the different patches for the protein N-terminus patches
(GLYP for glycine, PROP for proline).

Best,
Leo 

-- 
Leonardo Giantini Trabuco
Ph.D. candidate
Center for Biophysics and Computational Biology
University of Illinois at Urbana-Champaign