[gmx-users] amber99sb in GROMACS vs amber99sb in AMBER

[Thomas Evangelidis]

Hi Oliver,

Apologies for the late reply. The comparison you have showed us has been
done for a DNA fragment. Do you believe that negligible errors can also be
obtained for proteins using the amber99sb force field?

thanks,
Thomas



On 22 November 2011 11:58, Oliver Grant <olivercgrant at gmail.com> wrote:

> Hi there,
>
> Acpype does the conversion for you and the results from their own testing
> are here:
> http://code.google.com/p/acpype/wiki/TestingAcpypeAmb2gmx
>
> For reproducing experimental data I would look in the original force-field
> publications.
>
> Oliver
>
>
> On Mon, Nov 21, 2011 at 8:21 PM, Michael Shirts <mrshirts at gmail.com>wrote:
>
>> > Is anyone aware of any benchmark analysis about the implementation of
>> the
>> > amber99sb force field (or any of its variants: 99sb-ildn, 99sb-nmr) in
>> > GROMACS and AMBER. I am interested to know in what extend the energies
>> > correlate and if the results agree with experimental data.
>>
>> Whether the results compare agree with experimental data is irrelevant
>> to the correctness of the implementation -- that has to do with the
>> validity of AMBER99sb to begin with.  The only question is, do GROMACS
>> and AMBER give the same energies for the same configurations?
>>
>> I actually do not know the answer, and would be interested to hear if
>> it's been tested.  http://ffamber.cnsm.csulb.edu/ does not appear to
>> have the very comprehensive tests that appear for earlier models at
>> the current time.  I SUSPECT there should not be a problem, since
>> AMBER99sb just changed a couple of torsions, so errors are unlikely
>> (though in theory possible).
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>
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-- 

======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com


website: https://sites.google.com/site/thomasevangelidishomepage/
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