VMD-L Mailing List
From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Thu Jan 29 2015 - 12:30:47 CST
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Hello,
I'm using vmd to call psfgen in order to patch a solvated structure and
create duplicate "dummy" atoms. I'd like psfgen to build the new atoms in
accord with patch's IC table and
without changing the existing ones. As such, I believe it should suffice to
"seed" the psfgen guesscoord command by explicitly setting a few atoms in
the chain as direct copies of existing atoms (these will be
non-interacting, so it is not a problem).
My script looks something like this:
# load psfgen and load psf and coordinates into psfgen and vmd (these must
be separate?)
package require psfgen
<load topology files with patch, etc.>
readpsf ...
mol load psf ..
# apply the patch (which adds new atoms) and regenerate bond/angle/dihedral
terms
patch ...
regenerate angles dihedrals
# "seed" the ic build by copying the atom CB to its copy CB1
set cb [atomselect top "segid PROT and resid 2 and name CB"]
set cbx [$cb get {x y z}]
coord PROT 2 CB1 $cbx # <-- PROBLEM HAPPENS HERE
guesscoord
writepsf ..
writepdb ...
however I seem to be missing something as to how Tcl and/or psfgen take the
coordinate values. The psfgen coord command keeps giving a standard usage
error:
arguments: segid resid atomname { x y z }
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over
I've tried a number of ways of reformatting the coordinates with puts or
expr or [], but I can't even tell what vmd/tcl *thinks* I am giving it.
Any help much appreciated,
Brian
-- Brian Radak Postdoctoral Scholar University of Chicago Department of Biochemistry & Molecular Biology Gordon Center for Integrative Science, W323A 929 E. 57th St. Chicago, IL 60637-1454 Tel: 773/834-2812 e-mail: radak_at_uchicago.edu
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- Reply: Axel Kohlmeyer: "Re: quick tcl question with vmd/psfgen"
- Reply: Josh Vermaas: "Re: quick tcl question with vmd/psfgen"
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