VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Sep 12 2008 - 02:51:03 CDT

In case you haven't figured this out, you need a space between
"segment C" and "{".

It's always easier for someone else to find typos. :)

On Sep 9, 2008, at 7:50 PM, Irene Newhouse wrote:

> 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 psfgen
> topology hemtop.txt
> alias residue HIS HSD
> alias atom ILE CD1 CD
> alias atom GLU OT1 OE1
> alias 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 HA
> patch PLO2 OA:0 HA:900 A:82
> #
> segment OB (o2b.pdb}
> coordpdb o2b.pdb OB
> patch PLO2 OB:0 HB:900 B:82
> #
> segment OC {o2c.pdb}
> coordpdb o2c.pdb OC
> patch PLO2 OC:0 HC:900 C:82
> regenerate angles dihedrals
> writepsf aida.psf
> guesscoord
> 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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