Subject: None

From: "Don Gregory" <[email-masked]>
Date: 1 Mar 1995 12:40:16 +0000

Subject:                               Time:12:35
PM
  OFFICE MEMO          None                                   Date:3/1/95

On March 1, McCarron wrote:
"Has anyone out there carried out amino acid mutations using BLOCK
If so do you know how to get around the problem of having interactions
between three blocks (blocks 2 and 3 containing different side chains)"?

Matthew,
When using the BLOCK facility within CHARMm, if you've successfully
assigned atoms to block 2 and 3 (by default, all atoms are initially
placed into block 1), and assigned a "lambda" value, then interactions
between blocks 2 & 3 are *already* excluded.  So I'm not quite
sure what difficulties you are having.
Another consideration you may wish to make, is that one is
not restricted to only 3 blocks, but can define numerous blocks.
In this instance however, you must use the explicit 'COEFF" commands
to specify the coefficients between each block.
If, however, you're doing a classic alchemical perturbation,
using 3 blocks, the lambda value will result in (for a lambda of 0.1),

interactions between block 1 and 2 = 0.1
interactions between block 1 and 3 = 0.9
interactions between block 2 and 3 = 0.0

This should be apparent in the matrix printout when leaving
the block facility in the CHARMm output file.

Don Gregory
Mgr. Life Science Applications
Molecular Simulations, Inc.