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

Sharapa dmitriy.sharapa at fau.de
Wed Aug 5 22:32:17 CEST 2015

Perhaps my explanation is very confusing, while i am trying to solve at 
least three problems at the same time.

1) I would like to use equilibrated solvent from virtualchemistry, not 
to get more errors by equilibrating attempts. Seems i can use "solvate" 
similar to http://blog.sciencenet.cn/blog-365047-808554.html (where was 
genbox as previous version) (i do not need mixing solvents, i saw your 
hexane-water tutorial, i am trying to understand them all at the same 
time). Anyway attempts to give to "solvate" a itp topology, like it was 
done in chinease manual for top file for genbox fails. Seems now its 
separated to "include", I'll read manual about that.
2) Single molecule - my solute. For which i have gaff topologies 
generated in Amber. I hope to use amb2gmx.pl to get sometopology that i 
can "include" after "insert-molecules" of my solute into the box of 
solvent that i describe in point 1.
3) Usage of GAFF in a simulation. This i will try to understand if i 
will manage to prepare box with solute and solvent and some sencefull 

Yes, i understand that for you its probably just usage of few trivial 
commands, but i am more used to another part of computational chemistry 
and so syntax and logic of Amber and Gromacs are very new, specific and 
confusing for me.

Thanks a lot for your advices.

On 05.08.2015 22:11, Justin Lemkul wrote:
> On 8/5/15 2:59 PM, Sharapa wrote:
>> Well, then i am confused again. "Liquid structure" pdb-s on 
>> virtualchemistry -
>> are they of any use directly in creating solvatebox, or they just 
>> shows what
>> system was equilibrated and topological parameters taken from?
> A pre-equilibrated box is just that - a liquid structure suitable for 
> further simulation or use as a solvent in another system.  As for 
> "creating solvatebox," I have no clue what you're talking about here.  
> Do you mean simply using that liquid as a solvent? That's 
> straightforward use of gmx solvate.  But you've alternately referred 
> to single molecules, AMBER topologies, GROMACS .itp files, and liquid 
> coordinate files, so I honestly have no idea what the primary question 
> is any more.
> -Justin
>> On 05.08.2015 20:49, Justin Lemkul wrote:
>>> On 8/5/15 2:31 PM, Sharapa wrote:
>>>> 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)
>>> My instructions were for how to create a starting liquid structure 
>>> (which will
>>> require LOTS of equilibration) from a single molecule. Hence
>>> "single_molecule.pdb" as its name, and "box.pdb" is the full liquid 
>>> structure
>>> with multiple molecules and however many atoms that winds up being.
>>> -Justin
>>>>>> 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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