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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> > AMBER.ambermd.org
> > 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 - 05:30:03 PDT
