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 <[EMAIL PROTECTED]> 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
