Dear Parul Sharma,
> I am trying to do explicit molecular dynamics calculations in 50% aqueous
> TFE/Water mixture. Could anyone please help me how to create the box?
If you look back few days ago in the Amber mailing list you will find
a similar discussion related to DMF/MeOH box. You will find these
discussions from the Archives of the Amber Mail Reflector. See:
http://archive.ambermd.org/200909/subject.html
look for "[AMBER] DMF solvent box"
However, you might have to wait few days so that the last messages appear.
You have to start by having a FF library for TFE; You could look in R.E.DD.B.
Using the download tool, you get:
Search... [Done]
Result(s) for search by Molecule name trifluoroethanol
Project name Trifluoroethanol
Project code W-15
Project name Trifluoroethanol
Project code W-16
Project name Organic solvent
Project code W-46
etc...
Here, to get the charges you might use 1 or 2 conformations...
You could add the FF atom type using Antechamber or using a scripting
based approach such as in:
http://q4md-forcefieldtools.org/REDDB/Projects/W-46/script1.ff
regards, Francois
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Received on Fri Sep 18 2009 - 17:30:02 PDT
