AMBER Archive (2009)

Subject: Re: [AMBER] how to make 50% aqueous TFE box?

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Sep 18 2009 - 19:22:35 CDT

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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