I believe the best approach would be to use the GAFF force field to assign
the atom types for the bonded and vdw parameters, and then do RESP charge
calculations to describe the e&s interactions. Maybe even antechamber can
give you some reasonable charges, but RESP calculations would be better.
Use antechamber to create your own library set for these molecules and
give GAFF ff as the force field parameter set you want to assign to these
molecules in antechamber.
If you want to do RESP charge calculation, you need to optimize these
molecules and then calculate the Electrostatic Potential surfaces.
Basically, I would suggest you to do the following:
1. Create these molecules in xLeap. Do not worry about the orientations.
2. Use antechamber to optimize the structures using AM1-BCC charge method.
The final structure should be much reasonable than xLeap created ones.
3. Depending on the QM software you have, optimize the structures
described in resp papers. Once you have the optimized geometry, you need
to calculate the MEP surfaces.
4. Use resp program to calculate the charges.
Step 3 and 4 are the hardest if you have never done any such calculations.
Thus, R.E.D. might be used here to accelerate the calculations, but
someone else should chime in here how to use that program.
Good luck,
Ilyas Yildirim, Ph.D.
-----------------------------------------------------------
= Department of Chemistry - 2145 Sheridan Road =
= Northwestern University - Evanston, IL 60208 =
= Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
= Website : http://ilyasyildirim.wordpress.com =
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On Tue, 18 Feb 2014, Ganesh Kamath wrote:
> My apologies:
>
> 1) RDX cyclotrimethylenetrinitramine: These are nitramines and energetic
> materials. http://en.wikipedia.org/wiki/RDX
> 2) PETN Pentaerythritol tetranitrate
> http://en.wikipedia.org/wiki/Pentaerythritol_tetranitrate
>
> thanks,
> ganesh
>
> On Tue, Feb 18, 2014 at 8:30 AM, ABEL Stephane 175950
> <Stephane.ABEL.cea.fr>wrote:
>
>> Hello
>>
>> We don't know ... What are RDX and PETN?
>>
>> Stephane
>>
>> --------
>> Stéphane Abel, PhD
>> CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221
>> Bat 528 Door 138C
>> Gif-sur-Yvette, F-91191 FRANCE
>> Phone (portable) : +33 6 49 37 70 60
>> ________________________________________
>> De : Ganesh Kamath [gkamath9173.gmail.com]
>> Envoyé : mardi 18 février 2014 15:23
>> À : AMBER Mailing List
>> Objet : [AMBER] Question about force field parameters for RDX and PETN
>>
>> Hi AMBER Folks,
>>
>> Is there a good set of parameters in GAFF for RDX and PETN. Could someone
>> point it out to me please.
>>
>> I appreciate the time and help.
>>
>> Regards,
>> Ganesh
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Received on Tue Feb 18 2014 - 07:30:03 PST
