VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Sep 01 2009 - 12:55:26 CDT

On Tue, 2009-09-01 at 21:28 +0430, Negar Ashari Astani wrote:
> Hi VMD experts
>
> My system consists of two walls and 3000 particles between them, I
> have inserted water molecules with GROMACS into my box and some of
> them are located behind my walls, Water molecules with z value more
> than 30 nm are outside the walls and should be omitted. I wrote the
> script below for this purpose but the output file is empty, I would be
> so grateful if i could have your comments on its problem:

nobody will have time to debug your script for you,
particularly not without having the full set of files
available.

i suggest you execute the script manually step by step
and use puts statements to validate the correctness and
result of each script statement. your script is not very
long or complicated, so it should be straightforward to do.

cheers,
   axel.
>
>
>
>
> mol delete all
> set sys [mol new input.pdb]
> set wal [atomselect $sys "resname WAL and name WL"]
> set walminmax [measure minmax $wal]
> set wal_maxz [lindex $walminmax 1 2]
> set outwat [atomselect $sys "resname SOL and name OW and
> z > $wal_maxz" ]
> set watminmax [measure minmax $outwat]
> set outwat_id [$outwat get resid]
> set finalsys [atomselect $sys "all and not resid
> $outwat_id"]
> $finalsys writepdb out1.pdb
>
>
>
>
> --
> Negar Ashari Astani
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Research Associate Professor
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.