There is. If you want a more hands-on approach to making force fields, you
can try the new mdgx tools as illustrated in these tutorials:
http://ambermd.org/tutorials/advanced/tutorial28/index.php
http://ambermd.org/tutorials/advanced/tutorial32/index.php
I haven't done boron, so it will be important to choose a QM basis set and
method that will work for it, but being such a light element it seems that
there's little holding you back, judging from the EMSL Basis Set Exchange.
You'll need some computers, but you've probably got access to a Beowulf
cluster, and an idea of how your molecules should move so that you can try
some initial configurations, then see what you get as the force field
evolves.
Dave
On Thu, Mar 8, 2018 at 8:58 AM, Barış Kurt <bariskurt007.gmail.com> wrote:
> Sir,
> almost all the addresses you provied has been crashed, (
> http://upjv.q4md-forcefieldtools.org/REDServer-Development/ says: We
> encountered a power cut the Feb. 12, 2018.
> http://upjv.q4md-forcefieldtools.org/REDServer-Development/Documentation/
> readme.txt
> says: not found exc...) especially R.E.D server and web site like a
> garbage: everything is too complex and it is not user-friendly software and
> webpage. I need a real and serious tool (with a good tutorial) to build a
> forcefield. Isn't there another way to generate a forcefield?
>
> Additonally, I looked at gaff2.dat file and I compared some data with
> gaussian09 results and I saw force constat units are different. Which
> units should I use if I want to write a *.dat file manually?
>
> As I mentioned above this is my PhD thesis, if there is no way to generate
> forcefiel please let me know.
>
>
> 2018-03-04 9:44 GMT+03:00 FyD <fyd.q4md-forcefieldtools.org>:
>
> > Hi,
> >
> > > there is no AMBER force field parameters for boron-carbon
> > > boron-oxygen and boron-hydrogen bonds. I have made optimization and EPS
> > > calculations on Gaussian about them, but I do not know how to develop a
> > new
> > > forcefield parameters. Is there a tutorial on this topic?
> > > Additonally, How do I calculate RESP loads for elements that do not
> have
> > > ForceField?
> >
> > After this literature search (vdW parameters ?) you could run PyRED at
> > RED Server Dev.
> > http://q4md-forcefieldtools.org/REDServer-Development/
> > You start from a PDB file for your models.
> > See http://q4md-forcefieldtools.org/Tutorial/Mini-HowTo-InputFiles.pdf
> >
> > RESP charges are derived and FF parameters are listed (known &
> > missing). By using the Re_Fit mode you can resubmit a job, and provide
> > these listed missing FF parameters using a frcmod.user file.
> >
> > regards, Francois
> >
> >
> > F.-Y. Dupradeau
> > ---
> > http://q4md-forcefieldtools.org/FyD/
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Mar 08 2018 - 10:00:02 PST
