[gmx-users] Solvatebox from itp GAFF organic solvents and amber solute.

Justin Lemkul jalemkul at vt.edu
Wed Aug 5 01:20:47 CEST 2015

On 8/4/15 12:09 PM, Sharapa wrote:
> Thanks a lot for fast answer.
> Yes, my fault, i didnt specify - i have coordinates for my molecule (from dft
> optimisation or from any other minimisation). And i have coordinates for
> equilibrated solvents from virtualchemistry. So i have coordinates, amber
> topologies for solute and itp for solvent. And no good ideas on combining them
> together in one solvatebox.



> On 04.08.2015 17:26, Justin Lemkul wrote:
>> On 8/4/15 10:45 AM, Sharapa wrote:
>>> Dear users and developers of Gromacs,
>>> I am new in MD in general and in Gromacs particulary.
>>> I want to make MD of small organic molecule in few organic solvents.
>>> My molecule containes Si and I made GAFF parameters for it. I would like to use
>>> GAFF in my simulation, expecting it to be not too bad for describing my system
>>> (that also contain pi-pi stacking).
>>> So far using ambertools I have .frchmod and prmtop files for my solute. I found
>>> .itp GAFF topology and .pdb GAFF Liquid structure files for solvents that i am
>>> interested in on http://virtualchemistry.org/ site. Nevetherless i still dont
>>> see the way how to create solvatebox with solute starting from data described
>>> above. I didn't found a tutorial describing similar procedures. If anyone can
>>> recommend me anything - i would be extremely thankful.
>> Because coordinates can't be built from topologies.  See
>> http://www.gromacs.org/Documentation/File_Formats/Coordinate_File#Sources for
>> ideas.
>> -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


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