VMD-L Mailing List

From: Jérôme Hénin (jerome.henin_at_uhp-nancy.fr)
Date: Fri Feb 18 2005 - 10:05:37 CST

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/