VMD-L Mailing List

From: Anirban Ghosh (anirbanz83_at_yahoo.co.in)
Date: Mon Oct 20 2008 - 06:27:06 CDT

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 Send free SMS to your Friends on Mobile from your Yahoo! Messenger. Download Now! http://messenger.yahoo.com/download.php