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

Justin A. Lemkul jalemkul at vt.edu
Wed May 20 20:35:18 CEST 2009

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?

Something is physically unrealistic about your system, leading to LINCS 
crashing.  Where did you get your parameters for the nitrile group?  If this is 
the common thread for the systems that crash, you can bet that whatever 
parameters you are using are not reliable.


> I would like some help on the matter
> Jocley
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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