[gmx-users] Solvatebox from itp GAFF organic solvents and amber solute.
dmitriy.sharapa at fau.de
Tue Aug 4 16:52:14 CEST 2015
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.
Thanks in advance,
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