Re: [AMBER] How to Develop New Amber ForceField For Borons

From: FyD <>
Date: Thu, 08 Mar 2018 20:14:44 +0100

Dear Kurt,

> almost all the addresses you provied has been crashed, (
> says: We
> encountered a power cut the Feb. 12, 2018.
> says: not found exc...)

Yes I know we have some problems these past weeks with our frontal/nas
server; Sorry for that...
I think it simply starts to be too old :-(

> 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?

garbage? serious tool? too complex?... well what can I answer to that?
  ... I hope our web site will soon back (next monday?) so that you
will be able to test it,
        and change your mind :-)
and charge derivation & FF generation for new models are all but
simple (just my opinion)...

> 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?

FF constant in Gaussian vs Amber *.dat file???
May be you could provide examples to clarify your mind.
I would first try to find vdW parameters compatible with Amber for Boron...

> As I mentioned above this is my PhD thesis, if there is no way to generate
> forcefiel please let me know.

Personally I would learn using RED Server Dev./PyRED ;-) when it will
be back...

regards, Francois

> 2018-03-04 9:44 GMT+03:00 FyD <>:
>> 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.
>> You start from a PDB file for your models.
>> See
>> 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

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Received on Thu Mar 08 2018 - 11:30:02 PST
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