[gmx-users] pdb2gmx -merge option take a *very* long time, and doesn't work ...

[Tsjerk Wassenaar]

Stephane,

As an exercise, try running pdb2gmx without redirection of the output...
Try to understand the programs and the options before trying to script
things (including redirecting input/output).

Tsjerk

On 5/23/07, Stéphane Téletchéa <steletch at jouy.inra.fr> wrote:
> time pdb2gmx -v -f 1HPV.pdb -o 1HPV_gro.pdb -p 1HPV_gro.top -i
> 1HPV_posre.itp -ff G53a6 -posrefc 100 -ignh -merge &>pdb2gmx1.log
>
> ... more than 15 minutes (and counting ...) while it is instataneous
> without the merge option.
>
> (my computer is a dual ahtlon 3800+, not that slow ...).
>
> As i understand, tt should merge the chain A and chain B into one chain
> (i may be wrong), so the molecule file in the top should contain only:
> Protein        1
> Not:
> Protein_A    1
> Protein_B    1
>
> In the end i get:
> pdb2gmx1.log
> 1HPV_posre_B.itp
> 1HPV_posre_A.itp
> 1HPV_gro.top
> 1HPV_gro.pdb
> 1HPV_gro_B.itp
> 1HPV_gro_A.itp
>
> Using gromacs 3.3.1.
>
> (attached the input pdb file for comparison).
>
> This is not *very* important, but since the merge option is here, i was
> trying to understand what is wrong.
>
> I've some specific questions on related topics, etc, i presume it would
> be better on bugzilla?
>
> Cheers,
> Stéphane
>
> (same message as already sent but with a compressed pdb).
>
> --
> Stéphane Téletchéa, PhD.                  http://www.steletch.org
> Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
> INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
> 78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623