Dear Francois,
I used your script to produce an *.off file for amber. When I tried to
produce the topology file, amber complained about missing CT-C-CT angle
parameter. I found
*CT-C-CT 63.0 117.0*
in google, but I don't trust this much. Do you have this angle parameter in
the acetone molecule?
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.ornl.gov
On Mon, Aug 24, 2009 at 3:31 AM, FyD <fyd.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.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.ambermd.org [mailto:amber-bounces.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.ornl.gov
>>>
>>
>
>
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>
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Received on Mon Aug 24 2009 - 15:00:07 PDT
