VMD-L Mailing List

From: Alexandre Suman de Araujo (asaraujo_at_if.sc.usp.br)
Date: Wed Mar 10 2010 - 06:03:01 CST

Hi Axel

The second suggestion worked very well.
But the use of mergestructs package resulted in problems. When I try to
use the following command:

mergestructs {file1.psf file1.pdb} {file2.psf file2.pdb} file3

I have the following error

wrong # args: should be "mergestructs"

When I try to call mergestructs without parameters, the GUI interface is
opened.
I tried to find the correct syntax but I have not success.
Do you mind what is happening?

Cheers

**************************************************************
Alexandre Suman de Araujo *
Faculdade de Ciências Farmacêuticas de Ribeirão Preto *
Universidade de São Paulo *
Dep. de Física e Química *
Grupo de Física Biológica * e-mail: asaraujo_at_fcfrp.usp.br*
Av. do Café, s/n° * e-mail: ale.suman_at_gmail.com *
CEP: 14040-903 * Phone: +55 (16) 3602-4172 *
Ribeirão Preto, SP, Brasil * Phone: +55 (16) 3602-4222 *
**************************************************************

Axel Kohlmeyer escreveu:
> hi alexandre,
>
> On Tue, Mar 9, 2010 at 1:24 PM, Alexandre Suman de Araujo
> <asaraujo_at_if.sc.usp.br> wrote:
>
>> Hi all.
>>
>> Is it possible to use MergeStructs plugin in Tk console or scripts?
>>
>
> yes.
>
>
>> If yes, which is the sintax should I use?
>>
>
> package require megstructs 1.0
> namespace import Mergestructs::*
>
> mergestructs {file1.psf file1.pdb} {file2.psf file2.pdb} file3
>
> that would require having the two molecules as external files.
>
> if you want to do this with internal data (perhaps after modifying
> bonding or atom types/names/coordinates) you can also try
>
> package require topotools 1.0
> namespace import TopoTools::mergemols
>
> set newmol [mergemols {0 1 2}]
>
> animate write psf file3.psf $newmol
> animate write pdb file3.pdb $newmol
>
> there are a few small improvements in the topotools package
> since vmd 1.8.7, so if you don't want to update to the latest
> VMD alpha version, you can download the updated package
> by itself from
>
> https://sites.google.com/site/akohlmey/software/topotools
>
> mergestructs uses psfgen and topotools uses the internal
> information that VMD has after loading a psf or similar topology
> format. so depending on what you are doing one of the two
> may be the better solution.
>
> cheers,
> axel.
>
>
>> Cheers
>>
>> --
>> **************************************************************
>> Alexandre Suman de Araujo *
>> Faculdade de Ciências Farmacêuticas de Ribeirão Preto *
>> Universidade de São Paulo *
>> Dep. de Física e Química *
>> Grupo de Física Biológica * e-mail: asaraujo_at_fcfrp.usp.br*
>> Av. do Café, s/n° * e-mail: ale.suman_at_gmail.com *
>> CEP: 14040-903 * Phone: +55 (16) 3602-4172 *
>> Ribeirão Preto, SP, Brasil * Phone: +55 (16) 3602-4222 *
>> **************************************************************
>>
>>
>
>
>
>