AMBER Archive (2009)

Subject: RE: [AMBER] parmchk

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Feb 09 2009 - 10:28:20 CST

Hi Bill,

You will need to calculate these parameters. I suggest looking at some of the original force field papers (The Cornell et al JAC 1994 paper is probably a good start). This and some of the papers it cites has details of how force fields are fit. Also take a look at the GAFF paper.

Ultimately you need to try varying this angle in an ab initio QM calculation and then vary the angle force constant and equilibrium value to reproduce the energy curve as closely as possible.

You could also potentially add parameters based on analogy with existing parameters for example C -OS-CT which is 60.0 117.0.

However, I also have a number of concerns with what you are describing.

1) Why are you using parm96.dat? - It is 'highly' recommended that you NOT use FF96. Most people now recommend you use FF99SB or FF03 both of which are based on the underlying parm99.dat file with a few modifications of backbone torsions.

2) Obviously CA-OS-CT is not part of a regular amino acid since it would be in the force field. So I am wondering where this parameter combination comes from. Is this from a ligand? If so you should probably try Antechamber and the GAFF force field in which case the atom types would be lower case. How did you assign these types?

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of s. Bill
> Sent: Monday, February 09, 2009 7:55 AM
> To: amber_at_ambermd.org
> Subject: [AMBER] parmchk
>
> I have a problem!!!
> when I check the parameter file:
> $AMBERHOME/exe/parmchk -i ***.mol2 -f mol2 -o ***.frcmod -p parm96.dat
> I found there are some parameters are missing.
> How should I fill it in?
> for example:
> CA-OS-CT 0.000 0.000 ATTN, need revision
> thanks in advance
> s.bill
>
>
>
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