Subject: RE: help with MMFF94 in CHARMM (solution)

From: Robert Jorissen <[email-masked]>
Date: Sun, 26 Nov 2000 14:05:11 +1100

Dear CCLers

I seem to have found a solution my problem and am posting my solution as a
courtesy to anyone who may have a similar problem. My problem was: when
using the MMFF94 forcefield in CHARMM, I could not reproduce the non-bonded
energies of molecules in the MMFF94 validation set (see
http://www.ccl.net/cca/data/MMFF94/). As Rebecca Rone suggested, the problem
was with some of the parameters. The default VDW cut-off is 8 Angstroms when
MMFF94 is used. This cut-off should be set to a number larger than the
molecule's largest dimension. Similarly, the treatment of electrostatic
energies requires a change in parameter. The default MSHIFt keyword should
be replaced by the TRUNCation keyword.

The following example script (adapted from one of the CHARMM test scripts)
illustrates this:

* BEWCUB.inp
* Test reading in one small molecule structure in .mrk format and
calculating
* its energy in CHARMM
*

! Set up MMFF94 forcefield for use
set 0 /p1/charmm/test/data/     ! input data directory
stream @0mmff_setup.str

! Read and generate the small molecule
open read form unit 1 name "BEWCUB.mrk"
read merck unit 1
close unit 1

generate

 write merck unit 6

! Calculate the MMFF energy of the molecule
update inbfrq 1 ihbfrq 0 CUTNB 999. CTOFNB 888. cdie e14fac 0.75 CTVTRN 888.
TRUNC
energy

stop

The CTVTRN 888. (VDW cut-off) and TRUNC (handling of long range
electrostatics) parts of the update command were the additions that seemed
to make everything work.

I have only tested a small portion of the MMFF94 validation set and so there
may be further problems I haven't picked up.

Robert Jorissen
Ludwig Institute for Cancer Research