I had a similar problem, since I had to simulate a mixture of water
and propylene glycol. I made PG by myself, optimizing the structure
and calculating charges by means of quantum chemistry (you can
calculate ESP and then calculate atomic charges with respgen utility
of amber). At the end, I create the library, since parmchk utility of
amber can give you parameters you need.
Now the simulation is going well.
If you want to know more, feel free to contact me.
Tommaso Casalini, PhD
Cfa Lab, Politecnico di Milano
Def. Quota "Mattei, Alessandra" <ale.mattei.uky.edu>:
> Dear Amber users,
>
> I would like to run a simulation of an organic molecule in ethanol.
> First I have to create an ethanol box, but in the amber library I
> could not find etoh.off. In addition, I think I need frcmod.etoh.
> I found tripos2.mol2 file and I should convert it to etoh.off. Could
> you please give me directions how to do that? Once I have etoh.off,
> how can I create frcmod.etoh which contains parameters for ethanol
> in order to be able to solvate the molecule in ethanol?
>
> Thanks in advance for your help.
> Regards,
>
> Alessandra Mattei
> Department of Pharmaceutical Sciences
> University of Kentucky
> Lexington, KY 40536
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Feb 03 2011 - 09:30:07 PST
