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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