VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Apr 14 2008 - 13:13:10 CDT

Yes. If you delete the sidechain and Calpha hydrogen, things should work.
Peter

Jorgen Simonsen wrote:
> 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 <mailto: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
>
>