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

Sharapa dmitriy.sharapa at fau.de
Tue Aug 4 18:09:26 CEST 2015

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

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