AMBER Archive (2009)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Aug 24 2009 - 15:13:33 CDT

Jose,

> 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'.

I forgot: you will find trifluoroethanol but not
tri-fluoride-methanol. When deriving 2 stage RESP charges for Amber
force fields the charges of 3 Fs are equivalenced in the 1st RESP
stage while they are frozen in the 2nd stage (this part is not that
obvious).

See the RESP inputs for trifluoroethanol:
SEARCH - DOWNLOAD SECTION
Search... [Done]
Result(s) for search by Molecule name Trifluoroethanol
Project name Trifluoroethanol
Project code W-15

Corresponding RESP inputs (2 molecular orientations; single conformation):
http://q4md-forcefieldtools.org/REDDB/uploadfile/W-15/input1.in
http://q4md-forcefieldtools.org/REDDB/uploadfile/W-15/input2.in

More complex is W-16 (2 conformations; 4 orientations).

regards, Francois

> 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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