VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Jun 16 2008 - 09:45:36 CDT

On Mon, 16 Jun 2008, Leonhard Henkes wrote:

LH> Hello VMD community,
LH> at the moment I try to remove all water atoms from a POPE membran created with VMD with the help of my script. Actually it doesn't, but I can't find out the failure .My script produces the following error:
LH>
LH> atomselectt0
LH> too many arguments specified
LH> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
LH>
LH> MOLECULE MISSING! Use resetpsf to start over.
LH> Info) VMD for LINUXAMD64, version 1.8.6 (April 6, 2007)
LH> Info) Exiting normally.
LH>
LH> What can I do to get rid of the problem ??
LH> The script looks like this :
LH>
LH> source "Config_leo.tcl"
LH> package require psfgen
LH> resetpsf
LH> readpsf $input_psf
LH> coordpdb $input_pdb
LH> topology top_all27_prot_lipid.inp
LH> pdbalias residue HIS HSE

LH> mol load psf $input_psf
LH> mol load pdb $input_pdb

why those two commands? a) mol load is obsolescent (and
the proper sequence would be 'mol new ...; mol addfile ...'
anyways) b) _both_ commands will create a new (top) molecule,
and c) you already were reading them before.

cheers,
   axel.

LH> set badwater [atomselect top "name OH2"]
LH> foreach segid [$badwater get segid] resid [$badwater get resid] {
LH> delatom $segid $resid
LH> }
LH> writepdb pdb $output_pdb
LH> writepsf psf $output_psf
LH> exit
LH>
LH>
LH> THX for your help !
LH> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.