[gmx-users] miscelle formation using ligands only

Chetan Puri chetanpuris at gmail.com
Sun Sep 13 09:47:12 CEST 2015

So it means that my topology file should not contain any heading such as
bonds, atoms, dihedral, and should only contain #include drug.itp of
various molecules with system name and number of various molecules.
Can I just make a box of water.pdb using packmol and use pdb2gmx to
generategenerate a topology with oplsa.ff and include drug.itp files in
that topology file.

On Sunday, September 13, 2015, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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
> --
> ==================================================
> 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
> http://mackerell.umaryland.edu/~jalemkul
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