Hi Francois,
many thanks. Let me go through these steps.
--- Lalit
On Sat, May 22, 2010 at 1:00 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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
>
>
>
>
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Received on Sun May 23 2010 - 21:30:02 PDT
