AMBER Archive (2009)

Subject: RE: [AMBER] acetone lib and frcmod files?

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Aug 24 2009 - 02:31:40 CDT

Jose,

You will find libraries for acetone, acetonitrile & methyl alcohol in
R.E.DD.B. The format of the FF library is the Tripos mol2 file format
which can be used in LEaP.
Example of projects are the R.E.DD.B. project W-46 for instance:
http://q4md-forcefieldtools.org/REDDB/projects/W-46/

Various approaches are proposed to derive charges: W-46 up to W-49
RESP 2 stages, ESP and RESP 1 stage

To load the FF libraries in LEaP you could use the following LEaP script:
http://q4md-forcefieldtools.org/REDDB/projects/W-46/script1.ff

More simple projects are also available for individual organic
solvents. Use the "Dowload projects" tool to search in R.E.DD.B.:

Search... [Done]
Result(s) for search by Molecule name Methanol
Project name Methanol
Project code W-32

regards, Francois

Quoting Ross Walker <ross_at_rosswalker.co.uk>:

> Hi Jose,
>
> Taking a few minutes to do a little background searching would have found
> you the following page:
>
> http://www.pharmacy.manchester.ac.uk/bryce/amber
>
> This has the majority of what you need. The others you should be able to
> build yourself fairly simply and then you can use either the GAFF force
> field (with the obvious caveats) or, assuming a literature search does not
> uncover currently published parameters that you can use you should be able
> to parameterize these up for yourself fairly easily since they are all small
> molecules.
>
> Good luck,
> Ross
>
>> -----Original Message-----
>> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
>> Behalf Of Jose Borreguero
>> Sent: Sunday, August 23, 2009 2:37 PM
>> To: amber mailing list
>> Subject: [AMBER] acetone lib and frcmod files?
>>
>> Dear Amber users,
>>
>> I need the lib and frcmod files for the following molecules. Please do
>> contact me if you can provide me with any of these files.
>>
>> acetone
>> acetonitrile
>> dmf (Dimethylformamide)
>> isopropanol
>> meoh (Methyl Alcohol)
>> tfm (tri-fluoride-methanol)
>>
>>
>> Best regards,
>>
>> Jose M. Borreguero
>> Postdoctoral Associate
>> Oak Ridge National Laboratory
>> P.O. Box 2008, M.S. 6164
>> Oak Ridge, TN 37831
>> Google-voice: 404-567-6035
>> Office: 865-241-3071 fax: 865-576-5491
>> Email: borreguerojm_at_ornl.gov

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