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

Sharapa dmitriy.sharapa at fau.de
Wed Aug 5 17:29:22 CEST 2015

Dear Justin,
Thanks a lot for your links.
I looked them once again (i googled them for few times while i am 
stucked with this problem) and still do not understand how they can help me.
I will try to go throw manual once again.

Best regards,

On 05.08.2015 01:20, Justin Lemkul wrote:
> 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.
> http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
> http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation
> -Justin
>> 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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