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

[Sharapa]

Thanks a lot, that was very usefull.
I will try to collected all collected theory in practice.

On 05.08.2015 20:08, Justin Lemkul wrote:
>
> gmx insert-molecules -ci single_molecule.pdb -o box.pdb -box X -nmol N
>
> will insert N molecules into a cubic box of X-nm edge length. That is 
> for pure solvent, and it's the same as the first step in creating a 
> mixed solvent (which is then followed by another round of gmx 
> insert-molecules to add the co-solvent).
Single_molecule - am i right that i should use pdb of liquid structure 
(that is a rather big cube of solvent with thousands of atoms in it)

>
>> 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?
>>
>
> That depends on what the .itp files contain.  If they have a 
> [defaults] directive, all the force field parameters, etc. then 
> they're self-contained and can be used as-is, then you're done. If 
> they require parameters from some parent force field (more likely, 
> since you're dealing with frcmod files), then you need to utilize them 
> in the context of whatever parent force field you were using in AMBER:
>
> #include (some AMBER force field)
> #include (whatever your solvent .itp is)
>
> etc.
>
> -Justin
>
>> Thanks in advance,
>> Dmitriy
>>
>> 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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