VMD-L Mailing List

From: Ramin Ekhteiari (ramin_ekh_at_yahoo.com)
Date: Tue Apr 01 2014 - 08:24:33 CDT

Hi, I would like to generate psf file for a dimer protein (i.e., chain A and B). I tried this tcl commands , package require psfgen topology top_all36_prot.rtf topology top_all36_cgenff.rtf pdbalias residue HIS HSE pdbalias atom ILE CD1 CD segment U {pdb protein.pdb} coordpdb protein.pdb U guesscoord writepdb test.pdb writepsf test.psf  But the it generates only for one chain not more. Would you please advise me on how to do it for both chains. Would be grateful for any help. Cheers, Ramin.