Re: [AMBER] How to generate boron atom paramaters?

From: FyD <>
Date: Sun, 12 Jan 2014 09:57:42 +0100

Dear Vaibhav Dixit,

> I would like to know if borazines and azaborines can be treated similarly?
> The bonding situations in these systems is known to be like benzene but
> lesser aromatic character with geometrical differences.

I just ran a quick run on benzene, borazine, 1,2-azaborine and
1,3-azaborine (1,4-azaborine?) using R.E.D. Python; it is easy to
compare the structures of the optimized geometries, the derived charge
values and to design a first FF.

You can set MEPTHOD_OPTCALC = "..." & BASSET_OPTCALC = "..." in the file to use a higher theory level in geometry
optimization (useful for comparing structures of the optimized

Then you can imagine empirical rules to refine your FF. R.E.D. Server
Dev./R.E.D. python will list the known & unknown FF parameters (atom
types with ? such as 'H?' means unknown atom type).

You can also provide a frcmod.user file as input for missing force
field parameters and set MOLECULE1-ATMTYPE = ... to defined the FF
atom types of your choice.


regards, Francois

> On Sat, Jan 11, 2014 at 8:12 AM, FyD <> wrote:
>> Dear Mengyuan Zhu,
>> > As my molecule has boron atoms, antechamber can not deal with it.
>> > How can I do? I have generated Gaussian output file with
>> > HF/6-31G*basis set. Thank you!
>> You might be interested running R.E.D. Server Dev./R.E.D. Python at
>> R.E.D. Python will perform RESP or ESP charge derivation.
>> Different models are available:
>> R.E.D. Python performs many other tasks see:
>> among them: atom name corrections, atom typing and force field (FF)
>> parameter determination.
>> In your case known FF parameters will be reported in a frcmod.known
>> file, while unknown FF parameters will be listed in a frcmod.unknown
>> file. The later file will help you to determine which parameters you
>> need to work on.
>> R.E.D. Server Dev. can also accept as input a frcmod.user file, which
>> can be used to provide unknown FF parameters to R.E.D. Python.
>> regards, Francois

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Received on Sun Jan 12 2014 - 01:00:02 PST
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