[gmx-users] miscelle formation using ligands only

Justin Lemkul jalemkul at vt.edu
Sat Sep 12 21:30:36 CEST 2015

On 9/11/15 11:59 PM, Chetan Puri wrote:
> I am using gromacs for the first time . I have installed gromacs 5.0.4
> version and i want to check a miscelle is formed or not using 5 different
>   ligands in different ratios. I have gone through all basic tutorials on
> how to use gromacs ( lysosyme,protein-ligand).
> But i am stuck with the problem of having ligands only for simulation due
> to no force field and topology file.
>                        I have tried to use packmol to pack a cubic box with
> all my different ligands in different ratios and generated a pdb file but
> without making a topology file i am stuck.
>            So if some one can suggest some possible ways  of doing it and i
> don't have much computational background of manipulating various file
> extensions of gromacs.

The only difference here is that you probably aren't going to be using pdb2gmx, 
so your topology will be one of your own creation.  In practice, the .top is 
probably just going to amount to a series of #include statements for the 
topologies of the various molecules you want to study.



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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