VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 18 2005 - 10:35:00 CST

Jerome,
  Since I didn't write Stride, I really don't know why they need the
Hydrogen bonds. It's a good bet they knew what they were doing when
they wrote that code however. I suspect that the progam will fail if
you take out that safety check. If you don't have a copy of the Stride
source code already, I can make one available to you if you want to
examine this more closely.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Feb 18, 2005 at 05:05:37PM +0100, Jérôme Hénin wrote:
> Hi John,
>
> On Friday 18 February 2005 16:49, John Stone wrote:
> > Jerome,
> > Stride doesn't like your structure, and is aborting because it couldn't
> > find any hydrogen bonds. They have a little bit of code that aborts the
> > secondary structure calculation if it doesn't find H bonds anywhere:
> > for( Cn=0; Cn<NChain; Cn++ )
> > PlaceHydrogens(Chain[Cn]);
> >
> > if( (NHBond = FindHydrogenBonds(Chain,Cn,HBond,Cmd)) == 0 )
> > die("No hydrogen bonds found in %s\n",Cmd->InputFile);
> >
> > Are your atom names for your hydrogens unusual for some reason?
>
> I don't think so, but since the peptide is short and sometimes extended, I'm
> not really surprised that Stride finds no H-bond. What is not very clear to
> me is the rationale behind that test on H-bonds. Would it be a problem to do
> without it?
>
> Jerome
>
> --
> Jérôme Hénin
> Equipe de Dynamique des Assemblages Membranaires
> Université Henri Poincaré / CNRS
> Tel : (33) 3 83 68 43 95 Fax : (33) 3 83 68 43 71
> http://www.edam.uhp-nancy.fr/ 

-- 
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