VMD-L Mailing List

From: Jorgen Simonsen (jorgen589_at_gmail.com)
Date: Mon Apr 14 2008 - 12:55:11 CDT

No - I have not put the atoms into the D-form so should I remove the group
for which I would like to create the D-form?

On Mon, Apr 14, 2008 at 5:26 PM, Peter Freddolino <petefred_at_ks.uiuc.edu>
wrote:

> Hi Jorgen,
> the internal coordinate entries only come into play if there are missing
> atoms when you run psfgen. Are there any missing atoms in your input pdb?
> And are the amino acids of interest already in the D form at that point?
> Best,
> Peter
>
>
> Jorgen Simonsen wrote:
>
> > Hi,
> >
> > I am trying to generate a topology file for a protein which contains
> > some D-amino acids - I change the topology file as according to the tutorial
> > but when I look at the amino acids they are still in the L-conformation as
> > if the internal coordinates of the topology file has not been read?
> > Is there a way to force the topology file to read the IC when creating
> > PDB and PSF ?
> >
> > Best
> > Jorgen
> >
> >