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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Received on Thu Jul 14 2016 - 05:00:03 PDT
