Subject: Re: CCL:CHARMm and CHARMM differences?

From: [email-masked] (Don Gregory)
Date: Mon, 8 Jan 1996 15:03:58 -0500

At 11:57 AM 1/4/96 +0100, Eldbjoerg S. Heimstad wrote:
>I have been using the MSI-version CHARMm and Harvard version
>CHARMM for simulations and see from the topology files (top_all22_prot.inp
>and AMINO(H).RTF) that there are some differences in atomic
>charges for the amino acids (I have not yet looked at the parameters).
>
>Is there any significant important differences in topology and parameters
>between these two versions?
>
[From D.Gregory: Protein & Simulations Product Marketing Manager, Biosym/MSI]
The most significant difference between these two "versions", is that they are,
in fact, different force-fields.  This brings up a whole, interesting
discussion about
what "tranferrablility" means in force-field technology.  Often times, I hear
of people asking for parameters for some molecule, or element, without
specifying what force field they intend to use with these parameters.
Big mistake.
For example, take these two force fields, the Harvard/Karplus-CHARMM
force-field 
supplied with CHARMM, and the B/MSI force-field, supplied with CHARMm.
Are they similar?  Yes.  Are their parameters interchangable?  Now there
is a tougher question.  My caution would be to say no, not so simply.
The B/MSI-CHARMm used the Harvard/Karplus-CHARMM force field as
a starting point, but then went on to add new parameters, and refine
existing parameters quite independently.  The reasons for this?  Primarily
because [then] MSI felt a strong desire by our customers to have a single
force-field that would be generally applicable to a wide variety of molecules,
especially mixed complexes of classic molecule types, such as
protein-drug, protein-nucleic_acids, carbohydrates, etc.
To be sure, others have developed related force fields that are much more
specific to a particular class of molecules (note the SHAPES and CHEAT force
fields for metals and sugars respectively).
In developing a force field that could more confidently be used with these
types of complexes, and perhaps be slightly less accurate with pure peptide
systems, the overall character of the force field changed.  
This is at the heart of the internally "consistent force field" concept
that was 
begun decades ago.
In the latest version of the MSI-CHARMm force-field, some of the most
significant
changes have taken place in the radii of ions and metals, while there have
also been numerous, perhaps less significant changes elsewhere.
Whenever a new version of the B/MSI-CHARMm force field is distributed,
we try to make a loud, bold statement to our existing users that they
SHOULD continue to use the previous force-field to complete the projects
they are currently working upon.  One of the last things you ever want to 
do, is to change force fields in the middle of a project.
It is up to companies such as ourselves, to ensure that classic problems
and benchmarks are still valid with each new force field, so that customers
can confidently use a new force-field when it is made available.
>
>I have used MSI-topology and parameters files with a parallel version
>of (academic) CHARMM -could that cause any problems?
>
As far as we know, the only difficulty anyone might have, in using the 
MSI-CHARMm force-field within the CHARMM program, is that one might
run out of array space when loading in the much larger MSI-CHARMm 
parameter set.  If not, there should be virtually no difficulty.
If anyone does find any problems, we hope they alert us through any of the
standard channels:
mail to myself: "[email-masked]"
mail to the support hotline: "[email-masked]"
or through the 1800 number, i.e.
1 800 756 4MSI  (756-4675)

Don Gregory