Subject: Re: Question on charges in CVFF on CCL

From: Ken Butenhof <[email-masked]>
Date: Tue, 26 Mar 2002 14:37:43 -0500

Hello CCL'ers,

In Insight II for all force fields except CFF, assignment of charges (and 
atom types) to each atom is done with the "Potentials" parameter block, 
which is accessed from the "FF" icon.  The Insight program assigns atom 
types and partial charges to each atom in the structure based on 
information in a residue library file (.rlb) if the residue is known or (if 
not found in a residue library file) from the bond increments found in the 
force field file based on the atom types.  The charge values present in the 
residue library file and the bond increments in the force field file
(.frc) are derived from experimental (usually crystallographic) data and 
quantum mechanical modelling.  The purpose of using a bond increment scheme 
for residues not in the residue library is that the local bonded 
environment (as described by the atom types) determines the atom centered 
charge.  The Gasteiger method first determines the overall charge of the 
system and then distributes that charge throughout the molecule (the 
Gasteiger method is available for use with Discover in Cerius2).  Note that 
CVFF was developed to reproduce peptide and protein properties.   The CFF 
force field has far greater support for highly funtionalized small molecules.
This information is available to all Accelrys users at 
http://www.accelrys.com/doc.

Ken

>Dear all the CCLers:
>     I am a user of InsightII of Accelrys(former MSI). When I perform
>comutations, such as molecular minization or dynamics,I often use CVFF 
>force field. I always
>use FF (ForceField). This command is activated on the left side by 
>clicking on the FF
>button. Then select Forcefield/Potentials and make sure that all of the 
>settings as
>follows.
>             Potential Action [Fix]
>
>             Partial Charge Action [Fix]
>
>             Formal Charge Action [Fix or Accept]
>
>     My question is how the partial charges of my molecules are computed?
>In my opinion,the partial charges are part of the CVFF force field. When CVFF
>is used, thepartial charges are automatically loaded from the system file. 
>This is
>quite different from MM2 (Tripos) method which often calculate partial 
>charge through
>Gasteiger-Huckel method for small molecules.Is this so? I have referred 
>several papers,
>but find no how the charges are computed.

Kenneth Butenhof, Ph. D.        phone: 800 756-4674
Principle Scientist             email: [email-masked]
Life Science Support            web:  www.accelrys.com/support
Accelrys