Hi Hector,
Sorry for the delay in replying. The last week was kind of crazy for me.
> I have a question about AMBER force field equation. I'm
> trying to
> calculate the Van der Waals and Electrostatic part of the equation and
> compare
> it with AMBER calculated value in the .out file. I used A and B values
> from the
> "parm99.dat" and charge "q" from the amino library files. I'm just
> running a 3
> atoms system (CA, C, O - no bonds) to check my calculation with AMBER.
> But my
> calculation and AMBER calculated values for Van der Waals &
> Electrostatic do not
> match. I wonder why. Please, any suggestions.
Are you excluding 1-2 and 1-3 interactions and scaling the 1-4's? Note just
about every single published version of the AMBER (and Charmm and Gromos)
equations are wrong since they do not correctly specify the nonbond sum as
excluding all bond and angle terms and scaling dihedral terms. Firstly, make
sure you are running a gas phase calculation in amber so you do not need to
worry about the complexities of PME etc. Then calculate the EEL terms as per
the equation except if the two atoms I,j have a bond, angle or dihedral
between them. This should then give you EEL energies that match, assuming
you use a dielectric of 1 and adjust for e0. Then go over all the unique
dihedrals and calculate the Eel interaction but divided by 1.2. This should
correspond to 14EEL in the sander output. Do the same for the VDW but scale
these by 2.0 - this should correspond to the 14VDW in the sander output.
Good luck,
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Sun Aug 22 2010 - 08:00:03 PDT
