VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Oct 20 2008 - 06:59:42 CDT

Hi Anirban,
are you sure that the residues are actually named URA in your input pdb?
Frequently uracil residues are named U in pdb files, or have some atoms
with incorrect naming; autopsf has some aliases that it applies to
circumvent common naming problems like this. Your first step should be
to make sure that your residue and atom names exactly match those in the
topology file.
Best,
Peter

Anirban Ghosh wrote:
> Hi ALL,
>
> I want to generate PSF files for a large no. of PDB files at a time.
> My molecules consists of URA residues. When I am generating the PSF
> files with the following script, then the URA molecules are not
> getting considered in the generated PSF file.
>
> ###################################
> package require psfgen
> resetpsf
>
> topology top_all27_prot_lipid_na.inp
>
> segment 1 { pdb 1.pdb}
> coordpdb 1.pdb 1
>
> guesscoord
>
> writepdb 1_new.pdb
> writepsf 1_new.psf
> ###################################
>
> However if I use the Autopsf plugin of VMD, then the output PSF files
> are having the URA residues. Why is this happening?
> I want to use the script as I need to generate a large no. of PSF
> files at a time. Please advice what is going wrong in the script.
>
>
> Regards,
>
>
>
> *Anirban Ghosh*
> *M.Tech Bioinformatics*
> *University of Hyderabad*
>
>
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