Dear Mannan,
> Thanks for the answer,
> How do I built the system with Glycerol or Glycerol water mix,
> What is the technique involved?
You need to get charges for Glycerol and a FF library; FF atom types
can be added afterwards. For Glycerol, you have many donor & acceptor
of H-bonds; this means you will get many different conformations
possible. The difficulty might be to select one or more; and find good
reasons for that...
You could look at polyols in R.E.DD.B. to get examples of RESP charge
derivation for polyols:
Use the "Download project" utility & search for keyword "Alcohol":
-- R.E.DD.B. code (if known)
-- Molecule keyword *
-- Molecule name
-- Author lastname
-- Theory level/Basis set
Text Alcohol
Among many others, see Glycol:
http://q4md-forcefieldtools.org/REDDB/projects/W-26/
etc...
To build the solvent box:
See
http://archive.ambermd.org/200909/0211.html
Or you search .
http://archive.ambermd.org/
using "Solvent Box"
regards, Francois
> --- On Sat, 13/2/10, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>
> From: FyD <fyd.q4md-forcefieldtools.org>
> Subject: Re: [AMBER] Glycerol Models
> To: "AMBER Mailing List" <amber.ambermd.org>
> Date: Saturday, 13 February, 2010, 2:15 PM
>
>
> Dear Mannan,
>
>> I would like to use glycerol instead of TIP3P water models in my
>> system of interest.
>
> You could try to build a box of glycerol or glycerol/water mixture.
> However, the problem with glycerol is its viscosity...
> Please see: http://pubs.acs.org/doi/abs/10.1021/jp076301d
>
> regards, Francois
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Feb 17 2010 - 15:30:03 PST
