VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Tue Sep 09 2008 - 13:50:10 CDT

I've been asked to do some MD on a heme protein, and I'm running into some problems. First I tried using a command file to do this:
 
package require psfgentopology hemtop.txtalias residue HIS HSDalias atom ILE CD1 CDalias atom GLU OT1 OE1alias atom GLU OT2 OE2
segment A { first NTER last CT2 pdb cha.pdb}coordpdb cha.pdb A#segment B { first NTER last CT2 pdb chb.pdb}coordpdb chb.pdb B#segment C{ first NTER last CT2 pdb chc.pdb}coordpdb chc.pdb C#segment HA {hemea.pdb}coordpdb hemea.pdb HA#segment HB {hemeb.pdb}coordpdb hemeb.pdb HB#
#segment OA {o2a.pdb}coordpdb o2a.pdb HApatch PLO2 OA:0 HA:900 A:82#segment OB (o2b.pdb}coordpdb o2b.pdb OBpatch PLO2 OB:0 HB:900 B:82#segment OC {o2c.pdb}coordpdb o2c.pdb OCpatch PLO2 OC:0 HC:900 C:82
regenerate angles dihedralswritepsf aida.psfguesscoord writepdb aida.pdb
exit
 
This goes through the process for chain a, then goes through chain b & crashes. The place at which it crashes was the same point as when chain a was finished & chain b started processing. The error message says:
 
reading coordinates from pdbfile chb.pdb for chain B
argument: segname {commands}
MOLECULE DESTROYED BY FATAL ERROR!
 
So I decided to use autopsfgen. It cannot place the heme coordinates. It produces a lovely protein, but all the heme atoms are at the origin.
 
I'm not fussy - help with either method suits me fine!
 
Thanks in advance!
Irene Newhouse
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