VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Jan 29 2015 - 13:56:45 CST

On Thu, Jan 29, 2015 at 2:49 PM, Brian Radak
<brian.radak.accts_at_gmail.com> wrote:
> 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),

it is coming from you trusting me getting the syntax right from memory. ;-)

if you (or me) had checked the lindex syntax we both would have seen
that the order of the arguments in the lindex command is the other way
around. i.e.:

> set cbx [lindex [$cb get {x y z}] 0]

JC got it right.

axel

>
> 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 

-- 
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.