On Fri, 2014-09-12 at 18:48 +0530, sunita.tifrh.res.in wrote:
> Dear Guys,
>
> After going through the literature I find ff99SB*-ILDN is the one which
> gives comparable result to the experimental observations.
>
> I am having Amber12 where leaprc of ff99SBildn, ff12SB etc are there but
> ff99SB*ildn is not there.
I've never heard of this force field before. When I pulled up one of
D.E. Shaw's papers mentioning ff99SB*ILDN [1], that force field had 3
citations: ff99SB, another citation, and then the original citation for
ff99SB-ILDN (i.e., there is no indication I see that this force field is
any different than ff99SB-ILDN).
> Can I get this force field ?
>
> Your help will be highly appreciated.
The only way a leaprc file defining this force field would exist would
be if someone had an interest in using that force field that was strong
enough to prompt them to make an frcmod file with the modifications. If
someone has done that, hopefully they will respond back with the
relevant files.
In the meantime (or in case you are the first person that monitors this
list that wants to use this force field), you may want to try to define
this force field yourself. This may actually be quite a bit easier than
you expect. I presume that if ff99SB*ILDN is actually different than
ff99SB-ILDN, it differs by only a small number of parameters. You can
implement these small changes in a new frcmod file that you load after
leaprc.ff99SBildn. You will probably learn a bit more about how tleap
works and setting up force fields in the process. Of course, you will
have to actually find the citation where the differences between
ff99SB*ILDN and ff99SB-ILDN to do this (as would _anybody_ interested in
doing this).
Hope this helps, and good luck!
Jason
[1]
http://www.sciencedirect.com/science/article/pii/S0006349511004097
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 12 2014 - 07:00:02 PDT
