[gmx-users] Problems with grompp and posre.itp in gromacs 4.0

Nuno Azoia nazoia at det.uminho.pt
Fri Oct 31 17:20:33 CET 2008

Hello every one!

I'm working with a trimeric system. When I use pdb2gmx the program
creates 3 different  itp files (protein_A.itp, protein_B.itp and
protein_C.itp) and the corresponding posre files (posre_A.itp,
posre_B.itp and posre_C.itp).

In gromacs 3.3.1 I never had problems with grompp and the posre.itp
files. But now I'm starting to use version 4.0 and I had soe problems
with grompp. I use the same comand line I used before

/gromacs/gromacs-4.0/bin/grompp -f mdp.mdp -po mdp-out.mdp -c
protein_solvent_box.gro -n index.ndx -r protein_solvent_box.gro -p
protein.top -pp protein-processed.top -o minimize1.tpr

and now I'm receiving a error message and I can not understand why:

Program grompp, VERSION 4.0
Source code file: futil.c, line: 527

Fatal error:
Library file posre.itp not found in current dir nor in default
(You can set the directories to search with the GMXLIB path variable)

As I'm was saying, I've used this command line in 3.3.1, for tha same
system with exactly the same file structure, and I never had problems,
and in the manual I can not see any diference in grompp.

I was wondering if there is anyone that can help me with this.

Just some information regarding my system:

in the protein.top file I have the lines

; Include chain topologies
#include "protein_A.itp"
#include "protein_B.itp"
#include "protein_C.itp"

In every of this itp files I have something like this

; Include Position restraint file
#ifdef POSRES
#include "posre_A.itp"

Thank you in advance for your help.

Nuno Azoia


Nuno Gonçalo Azoia Lopes

Laboratório de Investigação em Acabamento
Departamento de Engenharia Textil
Universidade do Minho
Campus de Azurém
4800-058 Guimarães

Tel: +351 253 510 280 - Ext: 517 289
Fax: +351 253 510 293

Mobile: +351 965 382 487
E-mail: nazoia at det.uminho.pt

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