[gmx-users] Molecule not minimized and NVT failure

Justin Lemkul jalemkul at vt.edu
Mon Apr 18 18:06:47 CEST 2016

On 4/18/16 12:02 PM, suniba wrote:
> Hello users I am doing protein-ligand MD using Gromos 43A1 and GROMACS 5.0.
> Therefore, following Justin's tutorial, I used PRODRG for ligand topolgy. I

After doing my tutorial, you should *not* be using PRODRG for topologies, for 
the reasons mentioned in that very tutorial.

> have drawn ligand using chemdraw and minimized the structure using chem3D.
> However, during energy minimization step in gromacs, the values converge
> earlier after 490 steps of minimization. This means that structure is not
> energy minimized properly. Also, during NVT, it crashes very early giving a

The number of steps has nothing to do with whether or not EM was effective.

> LINCS warning which is posted frequently in mailing list and the 'water'
> molecule not settled error. I have gone through all the solutions and
> according to my knowledge, the problem is with minimization. I am confused
> now how to minimize the structure properly to avoid the error. The long bond
> warning might also arise due to bad minimization? Any suggestions please. If
> require I can paste the ligand co-ordinates.

Ligand coordinates will tell us nothing of use.  The topology is more 
instructive, but in general go through: 

If your topology is straight from PRODRG, that's suspect #1 on my list.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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