Dear List,
I am sorry to bring up this query again on implementing ff99SB*-ildn which
was posted by some users in 2014 on the mailing list (
http://archive.ambermd.org/201409/0260.html).
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. It states "The potential associated with dihedral
angle ψ has been corrected according to Best and Hummer;(14) the correction
has been applied to all residues, including Gly and Pro, same as in paper 1
(12) (we have verified that the outcome does not depend on whether the
correction is extended to glycines and prolines).”
If I refer to reference 14 (Best and Hummer,2009), the modifications are
parameter
ff99SB**k*ψ (kcal/mol)
0.1788δψ (deg)
105.
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 could not figure out the modifications.
I am not sure how to implement those modifications above using ParmEd? Do I
have to delete all dihedral terms first?
Looking forward to your suggestions,
Many thanks,
Neha
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Received on Thu Jul 14 2016 - 00:00:04 PDT
