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

Sharapa dmitriy.sharapa at fau.de
Wed Aug 5 19:58:21 CEST 2015

Constructing solvent from itp files and pdb provided from 
virtualchemistry, (not making water or methanol solventbox that seems to 
be well automatizised) seems to me to be most untrivial (probably due to 
luck of experience).
Taking topologies from amber seems to be more trivial procedure, with 
amb2gmx.pl, but is it independent from forcefield. Dont i have to 
specify in calculation GAFF ?, and if yes - i dont see it as typical 
Gromacs forcefield, should i make smth extra for enabling GAFF?

Thanks in advance,

On 05.08.2015 19:38, Justin Lemkul wrote:
> On 8/5/15 11:23 AM, Sharapa wrote:
>> 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.
> I don't understand what the problem is.  You say you have topologies 
> and coordinates, so what's missing?  You have coordinates for a single 
> molecule, but not a full box?  That's trivial to construct with gmx 
> insert-molecules or genconf -nbox. All of that is described in those 
> links.
> -Justin
>> Best regards,
>> Dmitriy
>> 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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