Re: minimization-problem

From: Karol Kaszuba (karol.kaszuba_at_moskit.uwm.edu.pl)
Date: Thu Nov 22 2007 - 10:18:12 CST

 Hello,

 Probably your psf file was not generated correctly.
 Each different chain has to be treated separately, for example:
 let's say that your protein consists of an A chain and B chain so
 1) write these chains to separate pdb files: chainA.pdb and chainB.pdb
 2) in your script (for psf generation) you should type:
 package require psfgen
 topology top_all22_prot.in
 pdbalias residue HIS HSE
 pdbalias atom ILE CD1 CD

 segment A {pdb chainA.pdb}
 coordpdb chainA.pdb A

 segment B {pdb chainB.pdb}
 coordpdb chainB.pdb B

 guesscoord
 writepdb all_protein.pdb
 writepsf all_protein.pdb

 Should be good,
 Regards,

 Karol

 

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