You may first compare "ff99sb-ildn" (without "*") from Amber and
Gromacs .. These should be identical ....
The * corrects only backbone dihedrals (in fact, only psi), so when you
compare "ff99sb*-ildn" from Gromacs with "ff99sb-ildn" from Amber,
compare separately the backbone and side-chain dihedrals (only backbone
should differ) ....
Vlad
On 07/14/2016 02:10 PM, Neha Gandhi wrote:
> Yes Dac is right. Probably uploading the files should help.
> On 14 Jul 2016 10:03 PM, "Vlad Cojocaru" <vlad.cojocaru.mpi-muenster.mpg.de>
> wrote:
>
>> Ah, Sorry .. Of course Dave is right... I missed that you were
>> comparing "ff99SB*-ildn" from Gromacs with "ff99sb-ildn" from Amber ..
>> I thought you were comparing your own implementation of"ff99SB*-ildn" in
>> Amber with the Gromacs implementation .... Mea culpa for missing the
>> detail ....
>>
>> So, no surprise you get different dihedrals if you compare 2 different
>> force fields ...
>>
>> Best
>> Vlad
>>
>>
>>
>> On 07/14/2016 01:50 PM, David A Case wrote:
>>> On Thu, Jul 14, 2016, Neha Gandhi wrote:
>>>> To reiterate, ff99SB*-ildn is available in GROMACS. I came across a
>> paper
>>>> (Biochemistry, 2016, 55 (12), pp 1784–1800) wherein they have
>> implemented
>>>> ff99SB*ildn in AMBER.
>>> Have you contacted Prof. Skrynnikov to try to get the exact files his
>> group
>>> using?
>>>
>>>> As a test, I tried preparing files in gromacs using ff99SB*-ildn and
>> then
>>>> converting to AMBER prmtop using gromber (parmEd). I also prepared
>> prmtop
>>>> file in AMBER using ff99SB-ildn for the same test peptide. However,
>> most of
>>>> the dihedral terms were strikingly different upon comparison in two
>> files.
>>> I think this is what you should expect: ff99SB*-ildn and ff99SB-ildn are
>>> different force fields (the "*" is very important).
>>>
>>> ....dac
>>>
>>>
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>>> http://lists.ambermd.org/mailman/listinfo/amber
>> --
>> Dr. Vlad Cojocaru
>> Computational Structural Biology Laboratory
>> Department of Cell and Developmental Biology
>> Max Planck Institute for Molecular Biomedicine
>> Röntgenstrasse 20, 48149 Münster, Germany
>> Tel: +49-251-70365-324; Fax: +49-251-70365-399
>> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
>> http://www.mpi-muenster.mpg.de/43241/cojocaru
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Thu Jul 14 2016 - 05:30:04 PDT
