VMD-L Mailing List

From: Brian Radak (brian.radak.accts_at_gmail.com)
Date: Thu Jan 29 2015 - 13:49:00 CST

Thank you for the replies.

That gets me closer I think. The following changes to the middle portion:

set cb [atomselect top "segid PROT and resid 2 and name CB"]
set cbx [lindex 0 [$cb get {x y z}]]
coord PROT 2 CB1 $cbx

give me the following new error:

bad index "5.249566555023193 5.02329158782959 -0.4891093969345093": must be
integer?[+-]integer? or end?[+-]integer?
can't read "cbx": no such variable

It is still hard to tell where this error is coming from (I'm more
accustomed to Python tracebacks),

Brian

On Thu, Jan 29, 2015 at 1:33 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Thu, Jan 29, 2015 at 1:30 PM, Brian Radak
> <brian.radak.accts_at_gmail.com> wrote:
> > 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 $cbx # <-- PROBLEM HAPPENS HERE
> >
> > guesscoord
> > writepsf ..
> > writepdb ...
> >
> > however I seem to be missing something as to how Tcl and/or psfgen take
> the
> > coordinate values. The psfgen coord command keeps giving a standard usage
> > error:
> >
> > arguments: segid resid atomname { x y z }
> > MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over
> >
> > I've tried a number of ways of reformatting the coordinates with puts or
> > expr or [], but I can't even tell what vmd/tcl thinks I am giving it.
>
> that is most likely because an atomselect function returns not just a
> simple {x y z} coordinate tuple, but a list of those, one for each
> atom in the selection. so what you get is not a list, but a list of
> lists, i.e. { {x y z} }.
>
> the simplest way to get rid of the additional braces would be to use:
>
> set cbx [lindex 0 [$cb get {x y z}]]
>
>
> axel.
> >
> > 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
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy.
> 

-- 
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