Hi Neha,
What you are saying argues against trusting conversion tools between
Gromacs and Amber (its good you did a thorough test, but many don't do
that) .... The thing is that if I am not mistaken all studies with
ff99SB-ILDN* have been done using the Gromacs implementation which was
probably done on top of the Gromacs implementation of ff99SB ... I have
no idea how well the people that implemented these force fields in
Gromacs tested them against Amber ... But you may be safest using also
the Gromacs implementation ...
We have been looking into using ff99sb-ildn* in amber for a while
(example this thread and others:
http://archive.ambermd.org/201409/0298.html) but we ended up using the
Buschweiler's NMR-based modifications of ff99SB instead of the
Best&Hummer mods. It worked for our purposes but we did not do any major
tests on protein folding or secondary structure propensities ....
At that time, Francesco Gervasio sent me his implementation of the
ff99sb-ildn* force field in Amber but we could not use it because of
some atom type incompatibilites (if I recall correctly, it was long ago)
....
In the meantime we switched to the ff14SB (which is now published).
However, some recent posts indicated some potential issues with the chi
dihedrals in aromatic residues which apparently do not appear in ff12SB
(its predecessor) ...
So, my advice would be: unless you really depend on that particular
force field, switch to what is available in Amber. There is probably no
"one best force field" out there and you may find issue with any of them
.... But using what is available in Amber for simulations with Amber
topology is safer than conversions and adaptations.
If you do insist on using ff99sb-ildn*, try to email Francesco Gervasio
and maybe you can adapt his implementation .... Then, if you compare
with Gromacs, you could also do a 1 energy point calculation with both
Gromacs and Amber on 1 core and see if you get the same numbers ...
(maybe its the topology conversion that fails)
Best wishes
Vlad
On 07/14/2016 08:47 AM, Neha Gandhi wrote:
> 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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--
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 - 01:00:02 PDT
