VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Nov 11 2008 - 22:33:13 CST

If you read a pdb file through a segment statement, psfgen applies the
same segment name to all atoms in that file, which is not what you want.
You need to either split each segment into a separate file and then read
them all separately, or generate separate psfs for your files and merge
them by using the readpsf command to read the two individual psfs.
Peter

Anirban Ghosh wrote:
> I am using the following script to use psfgen:
> ------------------------------------------------------------
> package require psfgen
> resetpsf
>
> topology top_cg_prot_watr.inp
>
> segment A { pdb CG_RES_TNF.pdb
> }
> coordpdb CG_RES_TNF.pdb A
>
> segment B { pdb cg_solvate.pdb
> }
> coordpdb cg_solvate.pdb B
>
>
> guesscoord
>
> writepdb CG_FINAL_TNF.pdb
> writepsf CG_FINAL_TNF.psf
> ----------------------------------------------------------------------
>
> *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:* Wednesday, 12 November, 2008 9:52:28 AM
> *Subject:* Re: vmd-l: Re:
>
> Are you using readpsf/coordpdb or segment to load the build molecules
> in psfgen?
> Best,
> Peter
>
> Anirban Ghosh wrote:
>
> ------------------------------------------------------------------------
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