From: Anirban Ghosh (
Date: Tue Nov 11 2008 - 21:59:01 CST

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 <> To: Anirban Ghosh <> Cc: VMD List <> 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. <*> Unlimited freedom, unlimited storage. Get it now, on