Dear Yuan,
> I found one post in the mailist said REDDB
> http://q4md-forcefieldtools.org/REDDB/index.php, should has its parameters.
> But I really can not find it in the "download project".
I never submitted the corresponding data to R.E.DD.B. as I should have
done it...
We have a problem with this type of huge charge derivation: the
corresponding submission in R.E.DD.B. is time consuming & error
prone... With R.E.D. IV and R.E.D. Server 2.0 we can now generate a
large force field topology database in a single job such as for
instance the calixarene project:
http://q4md-forcefieldtools.org/REDDB/projects/F-87/ with more than
100 input molecules! However, the submission procedure in R.E.DD.B.
does not efficiently handle such a large amount of data.
This problem of submission in R.E.DD.B. is now a priority for our
q4md-forcefieldtools project; a student is working on it. Once this
problem solved/the program written (one month or so) we will release a
major update of R.E.DD.B.; not only about these regular cofactors,
with add-ons of other cofactors deriving from the main project...
etc...
During that time - if you want to try our data I can obviously send
you the FF library file to your personal email. We have two versions
of FF libraries; for the Cornell et al. or Duan et al. FF; Just let me
know which version you want to try.
Concerning geometry optimization of multiply charged molecules, I
would vote for following a building bock approach (i.e. the approach
we have used to study all these cofactors - by splitting the big
molecule into elementary building blocks) since the conformation after
geometry optimization of these multiply charged/large molecule is
unlikely to be representative... Just my personal opinion ;-)
regards, Francois
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Received on Thu Apr 14 2011 - 12:30:03 PDT
