[gmx-users] Help with nitrile group in complx protein-ligand md

Jocley Araujo gromacsjocley at gmail.com
Wed May 20 20:32:22 CEST 2009

I had a problem with mdrun while trying to run trajectories for protein
ligand complexes. I`ve already done successful calculations with 60
complexes, unfortunately 4 complexes gave the following error. The entire
output is too big to copy, so I have only copied the error part. But lots of
numbers appear before this error.

Program mdrun, VERSION 4.0.4
Source code file: constr.c, line: 136

Fatal error:
Too many LINCS warnings (1522)
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem

These ligands all have in common the nitrile group linked to an aromatic
ring. I am using the gromos 53a6 forcefield. The minimization step ran
normally for these complexes, so I only had problems when I tried to run the
md simulations. I have alreay tryed some of the solutions given by the gmx
user`s list like subtituting LINCS for SHAKE. Maybe my error has something
to do with the nitrile group. Has anyone had any problem like this before?

I would like some help on the matter

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