VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Nov 11 2008 - 22:07:42 CST

In that case, could you give a couple example lines of the error
messages you mention?
Best,
Peter

Anirban Ghosh wrote:
> Yes the segments have unique names...the protein has 3 segnames A, B
> and C and the water CG beads have senames as WT1, WT2,...WT8
>
>
> *Anirban Ghosh*
> *M.Tech Bioinformatics*
> *University of Hyderabad*
>
>
> ------------------------------------------------------------------------
> *From:* Peter Freddolino <petefred_at_ks.uiuc.edu>
> *To:* Anirban Ghosh <anirbanz83_at_yahoo.co.in>
> *Cc:* VMD List <vmd-l_at_ks.uiuc.edu>
> *Sent:* Tuesday, 11 November, 2008 10:00:47 PM
> *Subject:* vmd-l: Re:
>
> 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*
> >
> >
> > ------------------------------------------------------------------------
> > Add more friends to your messenger and enjoy! Invite them now.
> <http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/>
>
> ------------------------------------------------------------------------
> Add more friends to your messenger and enjoy! Invite them now.
> <http://in.rd.yahoo.com/tagline_messenger_6/*http://messenger.yahoo.com/invite/>