AMBER Archive (2009)

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

From: Jose Borreguero (borreguero_at_gmail.com)
Date: Mon Aug 24 2009 - 07:56:51 CDT

Hi Francois,

I couldn't find a search feature under the R.E.DD.B homepage. After reading
your message I noticed you had done a search on the site, so I went back and
could find a search service under 'download projects'.
Thank you so much!

On Mon, Aug 24, 2009 at 3:31 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:

> 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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