VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Nov 11 2008 - 10:30:47 CST

Do all of your segments have unique names?

Peter

Anirban Ghosh wrote:
> Hi ALL,
>
> I am trying to build a RBCG model of a 3-chain protein solvated in
> water. For that I am separately building the CG models for the protein
> and water and then trying to combine them using a psfgen script to
> generate the final CG PDB and PSF files. However VMD is not building
> all the water CG beads and showing an error "Duplicate entries" and in
> the final CG PDB many water CG beads are missing leaving huge voids
> inbetween. My water box contains around 16000 CG beads but the final
> structure along with the protein has only around 7000 water CG beads.
> Please suggest a solution. I am using VMD 1.8.7. alpha version. Thanks.
>
> Regards,
>
>
>
> *Anirban Ghosh*
> *M.Tech Bioinformatics*
> *University of Hyderabad*
>
>
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