AMBER Archive (2008)

Subject: Re: AMBER: organic solvents

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sat Nov 15 2008 - 01:56:30 CST


Hello Marcelo,

> Im trying to perform some simulations in different organic solvents,
> such as acetonitrile and DMSO.
> Is there any database of organic solvents for using in MD simulations?

You will find many examples of organic solvents in R.E.DD.B.
http://q4md-forcefieldtools.org/REDDB/
i.e. not only acetonitrile & DMSO. More will come:
http://q4md-forcefieldtools.org/REDDB/uploadfile/W-80/

You can use the "Download project" tool to perform a search using
"Molecule keyword" (Molecule keyword = Solvent; Molecule keyword =
Sulfoxide; Molecule keyword = Nitrile). You can use "Molecule name =
dimethylsulfoxide" or "Molecule name = acetonitrile" as well.

You will find also a new seach tool "Theory level/Basis set".

See for instance:
http://q4md-forcefieldtools.org/REDDB/up/W-1/
...
http://q4md-forcefieldtools.org/REDDB/up/W-46/
  up to
http://q4md-forcefieldtools.org/REDDB/up/W-49/

For a solvent, you will find different force field libraries depending
on the procedure used to derive the atomic charges. If you get lost
between the similar projects available in R.E.DD.B. for a same
solvent, read the Abstract (Project summary) and look at the Keywords
used during the charge deviation.

In each R.E.DD.B. project, a force field library is in the Tripos mol2
file format, which can be directly used in LEaP (sleap, tleap,
xleap...) or VMD...
You can use the LEaP script available in a project to load the
selected force field library in LEaP as provided in:
http://q4md-forcefieldtools.org/REDDB/up/W-46/script1.ff

I hope this helps,
regards, Francois

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