Yuan,
> 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.
You want the FF libs for the Cornell et al. FF which was updated,
modified and re-modified; last modification (ff99SB): Hornak et al.
> Please send me which you think is proper. And I would be very thankful to
> know some of their differences.
I will send you several FF libs; if you want more just ask...
regards, Francois
> 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 - 22:30:02 PDT
