AMBER Archive (2009)

Subject: RE: [AMBER] Regarding Urey-Bradley term in amber calculation

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Nov 24 2009 - 10:36:49 CST

Hi Aneesh,

We have recently completed adding support for the CHARMM force field, which
includes Urey-Bradley terms to the PMEMD software in AMBER v10.0. Sander
will also be supported in AMBER v11.0.

The approach is described in the following manuscript:

Crowley, M.F., Williamson, M.J., Walker, R.C., "CHAMBER: Comprehensive
Support for CHARMM Force Fields Within the AMBER Software", Int. J. Quant.
Chem., 2009, 109, 15, 3767-3772.

You can get the pdf from here:

http://www.wmd-lab.org/publications.htm

The tool to create the necessary modified prmtop files (from charmm psf
files), called Chamber, will be made available as part of AMBERTools 1.3.

Bugfix.26 on the AMBER website: http://ambermd.org/bugfixes10.html includes
patches to add support for the Charmm force field to PMEMD. This includes
support for Urey-Bradley terms. The additional prmtop sections look like
this:

------------------------------------------

%FLAG CHARMM_UREY_BRADLEY_COUNT
%COMMENT V(ub) = K_ub(r_ik - R_ub)**2
%COMMENT Number of Urey Bradley terms and types
%FORMAT(2i8)
      24 5
%FLAG CHARMM_UREY_BRADLEY
%COMMENT List of the two atoms and its parameter index
%COMMENT in each UB term: i,k,index
%FORMAT(10i8)
       2 5 5 3 5 5 4 5 5
5
       8 2 5 9 2 5 10 2 8
9
       1 8 10 1 9 10 1 15 18
2
      15 19 2 15 20 2 18 19 1
18
      20 1 19 20 1 25 28 2 25
29
       2 25 30 2 28 29 1 28 30
1
      29 30 1 25 32 3 25 33 3
32
      33 4
%FLAG CHARMM_UREY_BRADLEY_FORCE_CONSTANT
%COMMENT K_ub: kcal/mole/rad**2
%FORMAT(5e16.8)
  0.54000000E+01 0.22530000E+02 0.50000000E+02 0.70000000E+02
0.20000000E+02
%FLAG CHARMM_UREY_BRADLEY_EQUIL_VALUE
%COMMENT r_ub: A
%FORMAT(5e16.8)
  0.18020000E+01 0.21790000E+01 0.23880000E+01 0.22250000E+01
0.20740000E+01

------------------------------------------

If you want to simply run the entire charmm force field in pmemd then the
process is fairly automatic. If instead you want to use the AMBER force
field but have additional Urey-Bradley terms then you will have to get your
hands dirty and do some hacking of the code. You will also need to manually
create the prmtop sections since leap does not support this. The hard work,
adding the energy and derivatives is done though so the rest should be
fairly straight forward.

Good luck,
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of aneesh cna
> Sent: Monday, November 23, 2009 10:48 PM
> To: AMBER Mailing List
> Subject: [AMBER] Regarding Urey-Bradley term in amber calculation
>
> Dear amber users,
> I would like to keep "Urey-Bradley" term in angle potential form , in
> which
> takes the form of a harmonic interaction between the i-k sites of the
> covalently bonded triplet
> i-j-k (angle). How can I add angle distance term ( i-k distance) in
> Amber
> functional form for angle bending?. Waiting for your valuable reply
>
>
> Thanks in advance
> Aneesh
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

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