Dear Francois,
Thank you so much for your patient explanation and kind offer!
The difference of Cornell et al. and Duan et al. FF is beyond my knowledge.
I want to use this with leaprc.ff99SB or leaprc.ff03.r1.
Please send me which you think is proper. And I would be very thankful to
know some of their differences.
Best Regards!
Yuan
On Thu, Apr 14, 2011 at 3:02 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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 - 14:30:03 PDT
