From chemistry-request:~at~:server.ccl.net Tue Mar 26 14:56:12 2002 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2QJuBp13194 for ; Tue, 26 Mar 2002 14:56:11 -0500 Received: (from kenb -8 at 8- localhost) by sd.accelrys.com (8.11.0/8.11.0) id g2QL3lm23088 for chemistry {*at*} ccl.net; Tue, 26 Mar 2002 13:03:47 -0800 Received: from iris105.sd.accelrys.com (iris105.sd.accelrys.com [172.30.40.105]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g2QL3kV23079 for < %-% at %-% nmh-inner.sd.accelrys.com:chemistry %-% at %-% ccl.net>; Tue, 26 Mar 2002 13:03:47 -0800 Received: from kenbutenhof-pc.accelrys.com by iris105.sd.accelrys.com via ESMTP (980427.SGI.8.8.8/930416.SGI) for id LAA06910; Tue, 26 Mar 2002 11:55:59 -0800 (PST) Message-Id: <5.1.0.14.2.20020326135642.01ed7e80 -x- at -x- 172.30.45.77> X-Sender: kenb -x- at -x- 172.30.45.77 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 26 Mar 2002 14:37:43 -0500 To: chemistry%!at!%ccl.net From: Ken Butenhof Subject: Re: Question on charges in CVFF on CCL Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_109215463==_.ALT" --=====================_109215463==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed 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: kenb %-% at %-% accelrys.com Life Science Support web: www.accelrys.com/support Accelrys --=====================_109215463==_.ALT Content-Type: text/html; charset="us-ascii" 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: kenb #at# accelrys.com
Life Science Support            web:  www.accelrys.com/support
Accelrys --=====================_109215463==_.ALT--