AMBER Archive (2007)

Subject: Re: AMBER: THF parameters

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Wed Dec 05 2007 - 14:42:29 CST

Dear Dr Case,

As Piotr said, R.E.DD.B. will handle more complex data...

R.E.DD.B. already stores:
- RESP & ESP charge values within a force field library (mol2 file
format) for new molecules and molecular fragments,
- Computational conditions used to derive those charges (to re-inforce
the reproducibility of the data available),
- Description of the charge derivation in an abstract,
- Cartesian coordinates (optimized by QM) of the molecules used in the
charge derivation procedure,
- Scripts to convert the Tripos mol2 force field libraries into OFF
and RTF force field libraries,
- Force field parameters,
- Any data (free format) the author of a R.E.DD.B. project wishes to
provide (pictures, tables etc...)

All this is already described in the R.E.DD.B. FAQ
http://q4md-forcefieldtools.org/REDDB/faq.php

A peer review system for the project submitted in R.E.DD.B. will be
initiated to re-inforce the quality of the data stored in R.E.DD.B. A
new version of the FAQ describing this peer review system will be
released next January...

Most of these pieces of information are described in the R.E.DD.B. paper @
http://nar.oxfordjournals.org/cgi/content/abstract/gkm887v1

Then, with R.E.D.-IV, R.E.DD.B. will store whole force fields and
force field topology databases for any type of biomolecules (big jump,
here). We should be ready to release six of those force fields as new
examples next January.

With R.E.D.Server, we will propose an automatic computation of RESP
and ESP charge values within force field libaries based on the last
version of R.E.D. (beta version), and an automatic submission of the
data generated in R.E.DD.B. to help users.

Finally, we propose tutorials to help deriving RESP and ESP charge
values, and using this Tripos mol2 file format within LEaP and AMBER.
http://q4md-forcefieldtools.org/Tutorial/
As you know, we also have incorporated new functionalities to use the
Tripos mol2 file format in LEaP and more generally in AMBER.

Best regards, Francois

Quoting Piotr Cieplak <cieplak_at_cgl.ucsf.edu>:

> Yes, there is a plan for going toward this direction, e.g. including
> force fields parameters, but resources are scarce.
>
> Piotr
>
>
> On Wed, 5 Dec 2007, David A. Case wrote:
>
>>>> I am planning to do some MD simulations with modified nucleic acids
>>>> and in particular abasic sites.
>>>> I have would like to know if anyone could tell me where i can find HTF
>>>> (tetrahydrofuran) force field parameters?
>>>
>>> You have many examples of solvents in R.E.DD.B.
>>> http://q4md-forcefieldtools.org/REDDB
>>> W-39 Pyrrole
>>> W-38 Furane
>>> W-37 Methanal
>>> W-36 Formamide
>>> W-35 Acetonitrile
>>> W-34 Ethanoic acid
>>> W-33 Propanone
>>> W-32 Methanol
>>
>> Are these "just" charges, or are they complete force field files? For the
>> former, is there a way someone could move toward the latter?
>>
>> ...thx...dac

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