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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--
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 - 05:30:02 PDT
