[gmx-users] miscelle formation using ligands only

[Justin Lemkul]

On 9/13/15 3:47 AM, Chetan Puri wrote:
> 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.

That's likely the best route, though you can approach it a number of ways.  For 
a system that is simply a mixture of small molecules, I think this is the 
cleanest approach, though.

> 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.
>

You can, but it's really trivial to do yourself without pdb2gmx:

#include "oplsaa.ff/forcefield.itp"
#include "oplsaa.ff/tip3p.itp"

[ system ]
water

[ molecules ]
SOL	X

where X is the number of molecules you have. That's all there is to it.

-Justin

> 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
> 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
>>
>> --
>> ==================================================
>>
>> 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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-- 
==================================================

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

==================================================