Dear Lalit,
> I need to run a simulation of two solvents: Water and 1,2-dichloroethane.
> So, does amber has a solvent box of 1,2- dichloroethane?
> Please let me know. If not, then please suggest a way (on how to get
> 1,2-dichloroethane solvent box) or any pointers in this direction?
- You first need to generate a FF library for your solvent molecule
(as an isolated molecule). You can use Antechamber or R.E.D. for that.
You can find examples of solvent in R.E.DD.B.
See
http://q4md-forcefieldtools.org/REDDB/Projects/W-46/ for instance.
You can also use the "Download projects" tools to search in R.E.DD.B.
Search project(s) by
-- R.E.DD.B. code (if known)
-- Molecule keyword Toggle "on"
-- Molecule name
-- Author lastname
-- Theory level/Basis set
Text Solvent
=> You will get various solvent & different approaches for RESP & ESP
charge derivation.
- Once you got the FF lib (you might use the .mol2 file format) with
charges, topology, atom & residue names and FF atom types, you solvate
the solvent molecule by itself in LEaP and save the results in the PDB
file format.
- Then you write a script: you will modify every even number (if you
want a 50:50 solvent:water box) of the solvent molecules: remove all
the atoms of the considered molecule, except one (the carbon in your
case since it is in the center of your solvent molecule) that you are
going to rename using the atom & residue name of the water model you
wish to use (TIP3P, ...)
- You load the FF libs of your isolated solvent molecule + that of the
water model you wish to use and then the new PDB file in LEaP, and
LEaP will add the missing atoms for all the water molecules. Then, you
save the crd & top files and you are ready to equilibrate (constant
volume & then constant pressure).
regards, Francois
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 21 2010 - 23:30:03 PDT
