[gmx-users] Solvatebox from itp GAFF organic solvents and amber solute.
dmitriy.sharapa at fau.de
Wed Aug 5 17:29:22 CEST 2015
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.
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,
>> topologies for solute and itp for solvent. And no good ideas on
>> combining them
>> together in one solvatebox.
>> 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
>>>> 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
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