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

Stéphane Téletchéa steletch at jouy.inra.fr
Wed May 23 13:26:35 CEST 2007

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
Protein_A    1
Protein_B    1

In the end i get:

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?


(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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