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

[David van der Spoel]

Jocley Araujo wrote:
> Hello
> 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
You need to define a virtual site.
If you have C1-C2#N3 you want to make a bond (constraint) between 1 and 
3, and define 2 as a vsite (check manual).

> 
> Jocley
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se