AMBER Archive (2006)

Subject: RE: AMBER: The plc.frcmod file in the old version tutorial

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Nov 13 2006 - 10:29:26 CST

Dear Fenghui,

> There is something I do not understanding:
>
> 1.
> BOND
> NB-CU 70.000 2.05000 #kludge by JRS
>
> What is the meaning of 70.000? And what is the meaning
> of 2.05000?

70.0 is the bond force constant.
2.05 is the equilibrium distance

See the amber equation in the manual. I also suggest that you read the
various papers that have been published on amber including the FF94 one.
 
> 2.
> ANGLE
> CU-NB-CV 50.000 126.700 #JRS estimate
> Does CU-NB-CV means the bond formed by CU, NB,CV with
> CU and CV at each side of NB?
>
> What is the meaning of 50.000? And what is the meaning
> of 126.700?

CU-NB-CV means angle between CU, NB and CV with NB forming the central atom.

20.0 is the force constant
and
126.7 the equilibrium angle.

> 3.
>
> DIHE
> X -NB-CU-X 1 0.000 180.000 3.000
> What will be the definition of X? What is the
> definition of -NB-CU-X? What is the meaning of
> 1,0.000, 180.000,3.000 separately?

X is treated as a wildcard. See the FF94 paper and all should become clear.

>
> 4.
> NONBON
> CU 2.20 0.200
> I think NONBON should mean nonbounded, then what is
> the definition of 2.20 and 0.200 separately?

These are van der Waals parameters. Again a good survey of the literature
surrounding Amber and the system you want to simulate should answer all of
your questions. Without doing this you are just wasting your time as you are
going to end up running simulations that are meaningless. A week spent in
the library before you start will likely save you months of effort.

/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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