Summary of Re: CCL:FlexX help needed



Hi Ibrahim and CCL users,
 I got some answers for the FlexX Formal Charges problem. I attached the
 answers for you.
 And my experiment carried out that we can set the
 flag of Assign_Formal_Charges to 0 (automatically assignment OFF) or
 1(automatically assignment ON) through the Graphic User Interface
 panel of Sybyl FlexX. Then we can assign formal charges manually in the
 ligand.mol2 file when flag is 0.
 Thanks for everyone's kindly help.
      -----Mingzhu
     Southern Methodist University
 On Wed, 22 May 2002, Ibrahim Moustafa wrote:
 >  Hello Pearl,
 >
 >     I'm interested in your question. Can you forward me the answers you'll
 > get?
 >
 >   Thanks,
 >  Ibrahim
 >
 > Name         :Ibrahim M.Moustafa
 > Mail address :Center for Biomolecular Science,
 >               BIOMOLECULAR SCIENCE BUILDING,
 >               North Haugh,St-Andrews,
 >               Fife,KY16 9ST
 >               Scotland,U.K.
 >          Tel :+44(0)1334-467257
 >       E-mail :im17.,at,.st-andrews.ac.uk
 >
 > On Tue, 21 May 2002, Pearl Zheng wrote:
 >
 > > Hi dear CCL users,
 > >
 > > I am using sybyl FlexX to docking a small molecule to the active site
 of
 > > an enzyme. But the assignment of formal charges automatically by FlexX
 > > only works well in simple case. My question is how can I assign formal
 > > charge by myself. The second question is can I use Gasteiger-Huckel
 > > charges while doing FlexX?
 > >
 > > All response are appreciated.
 > >
 > >    ---Mingzhu
 > >
 > >
 > >
 > >
 > > -= This is automatically added to each message by mailing script =-
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 > >
 > >
 > >
 > >
 > >
 > >
 >
 
From jle.,at,.world.std.com Thu May 23 17:51:34 2002
 Date: Wed, 22 May 2002 06:39:11 -0400 (EDT)
 From: Joe M Leonard <jle.,at,.world.std.com>
 To: Pearl Zheng <zmz.,at,.jacobus.chem.smu.edu>
 Subject: Re:  CCL:FlexX help needed
 If you are using FlexX from within Sybyl, I think there is
 a way to generate formal charges for ligands before sending
 them to FlexX (check the options of the charge command).  Using
 partial charges affects the FlexX score and should not be used
 (the CScore options in Sybyl handles this).
 I am not sure whether the actual results are affected by
 using partial charges, but the FlexX energies are.  Note that
 it has been a while since I did this, so I am working from
 memory.
 Joe
 From Holger.Claussen.,at,.biosolveit.de Fri May 24 09:02:34 2002
 Date: Wed, 22 May 2002 15:09:36 +0200
 From: "[iso-8859-1] HolgerClaußen"
 <Holger.Claussen.,at,.biosolveit.de>
 To: 'Pearl Zheng' <zmz.,at,.jacobus.chem.smu.edu>, chemistry.,at,.ccl.net
 Subject: RE: FlexX help needed
     [ The following text is in the "iso-8859-1" character set. ]
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 Dear Pearl Zheng!
 You can set the formal charges of the ligands by any external tool, e.g.
 using Sybyl and you may even edit the ligand input file manually. Then
 you have to set the parameter ASSIGN_FORMAL_CHARGES to 2, so that FlexX
 uses the formal charges of the input file.
 The parameter ASSIGN_FORMAL_CHARGES can be set in two ways:
 1. interactively or in a batch script with the command SET
 2. in the config file that can be found here:
 $TA_ROOT/FlexX/tables/flexx_siteid_conf.dat
 In order to improve the automatic assignment of formal charges by FlexX,
 you can modify the file $TA_ROOT/FlexX/static_data/fcharges.dat, e.g. by
 adding another sub graph for your special case(s).
 FlexX uses only formal charges for docking. Partial charges cannot be
 used at all. Partial charges may even disturb the docking calculations
 if they are given in the ligand input file by mistake. Thus we advise to
 set the Parameter ASSIGN_FORMAL_CHARGES to 2 if the formal charges shall
 not be set automatically by FlexX (ASSIGN_FORMAL_CHARGES 1).
 If the Parameter ASSIGN_FORMAL_CHARGES is set to 2 FlexX checks, if the
 given charges are formal charges and if FlexX detects partial charges it
 assigns formal charges automatically.
 Best Regards,
 Holger Claußen
 FlexX Developer Team
 ________________________________________________________________________
 ____
        _________
                / _________          Dr. Holger Claussen
            Bio \ \                  Senior Research Scientist
        ________/ / olve
                  \________          BioSolveIT GmbH, An der Ziegelei 75
      I N F O R M A T I O N -        53757 St. Augustin, Germany
      - - T E C H N O L O G Y
                                     Tel: +49 - 2241 - 973 66 65
                                     Fax: +49 - 2241 - 973 66 88
        www.biosolveit.de            holger.claussen.,at,.biosolveit.de
 ________________________________________________________________________
 ____
 > -----Original Message-----
 > From: Computational Chemistry List [mailto:chemistry-request.,at,.ccl.net]
 On
 > Behalf Of Pearl Zheng
 > Sent: Tuesday, May 21, 2002 9:40 PM
 > To: chemistry.,at,.ccl.net
 > Subject: CCL:FlexX help needed
 >
 > Hi dear CCL users,
 >
 > I am using sybyl FlexX to docking a small molecule to the active site
 of
 > an enzyme. But the assignment of formal charges automatically by FlexX
 > only works well in simple case. My question is how can I assign formal
 > charge by myself. The second question is can I use Gasteiger-Huckel
 > charges while doing FlexX?
 >
 > All response are appreciated.
 >
 >    ---Mingzhu
 >
 >
 >
 >
 > -= This is automatically added to each message by mailing script =-
 > CHEMISTRY.,at,.ccl.net -- To Everybody  | CHEMISTRY-REQUEST.,at,.ccl.net --
 To
 > Admins
 > MAILSERV.,at,.ccl.net -- HELP CHEMISTRY or HELP SEARCH
 > CHEMISTRY-SEARCH.,at,.ccl.net -- archive search    |    Gopher:
 gopher.ccl.net
 > 70
 > Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan:
 > jkl.,at,.osc.edu
 >
 >
 >
 From thomas.steinbrecher.,at,.physchem.uni-freiburg.de Fri May 24 09:03:29 2002
 Date: Wed, 22 May 2002 18:05:30 +0200
 From: Thomas Steinbrecher
 <thomas.steinbrecher.,at,.physchem.uni-freiburg.de>
 To: Pearl Zheng <zmz.,at,.jacobus.chem.smu.edu>
 Subject: Re: CCL:FlexX help needed
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 Greetings,
 you can edit the formal charges in your mol2 file. But you
 should be aware that FlexX handles charges in a very very
 simple manner. So assigning charges in smaller increments
 than ~1/3 should not change the calculated results.
 If you edit your "config.dat" you will find a parameter
 called "ASSIGN_FORMAL_CHARGES". Set it to 0 instead of 1 or
 2 and FlexX should take the charges as set in the mol2
 file.
 Hope that helps,
 Thomas