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

[Sharapa]

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?

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
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>