[gmx-users] How to add a repulsive harmonic potential through define virtual atom?

Justin Lemkul jalemkul at vt.edu
Wed Jul 8 02:35:41 CEST 2015

On 7/7/15 2:54 PM, masoud aliyar wrote:
>   Hello dear GMX users I want to predict the probability binding of ligand
> to protein by unguided simulation. But when I increased concentration of
> ligand in the simulation box, the ligands has aggregated. So I decide to
> add repulsive potential between some atoms of ligands. I had search the
> archive of GMX-User mailing list and saw this question: How to add a
> repulsive harmonic potential?(1) , and read its answers. Finally according
> to the Justin’s Solution I defined one new ATOM in [atomtype] section and
> placed it in the [atoms] section of my ligands topology file (lig.itp).
> Then I defined the added atom as virtual atom in [virtual_sitesn] section.
> Then I create a new topology file (ligand-parameter.itp) that includes
> [atomtype] section of ligands (has cut from ligand topology files) and
> [nonbond_params] section. Also I added coordination of these new atoms in
> my complex coordination file (Conf.pdb). When I run command gmx mdrun -v
> -deffnm em got this error: Software inconsistency error: The mass of a
> vsiten constructing atom is <= 0. Can anyone help me to fix this error? Log
> file of what I do is here (log) (Files are in download links)   1-
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-April/096469.html
> Download
> links :  http://d01.megashares.com/dl/Jt8d7PZ/lig.itp

You can't introduce [nonbond_params] in the middle of a [moleculetype] 
directive; it's surprising that grompp even parses the topology.

I see nothing obviously wrong with the virtual site construction but I have 
never used the [vsitesn] type.  See if another constructing geometry works.


> http://d01.megashares.com/dl/LguyLcH/ligand-parameter.itp
> http://d01.megashares.com/dl/FHhKyVe/conf.pdb
> http://d01.megashares.com/dl/aIEDwDN/log


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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