Re: [ccp4bb]: Bond duplication error and extra density for chlorines

[Daan Virtual <vdava@davapc1.bioch.dundee.ac.uk>]

***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***


Hi

You don;t mention how you made your topology? If you did it manually
there's a suggestion there that you didn;t define your atoms properly.
Perhaps try triclosan from the HICUP server
(http://xray.bmc.uu.se/hicup/)

or put

  O
  |
C=C-C-O-C-C=C
|   "   "   |
C=C-C   C-C=C-Cl
|       |
Cl      Cl

into the PRODRG server at
http://davapc1.bioch.dundee.ac.uk/prodrg
and try the resulting CNS topology and parameter file.

cheers

Daan



On Fri, 13 Dec 2002, P. LAKSHMI SWARNA MUKHI wrote:

> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
> dear CNS users,
>
>       when i am using cns to put triclosan and refine my data i am getting
> an error
>
> PARRDR-ERROR: duplication of bond C_10 C_12
>  %PARRDR-ERROR: duplication of bond C_5  C_6
>  %PARRDR-ERROR: duplication of nonbonded entry C_5
>  %PARRDR-ERROR: duplication of nonbonded entry C_6
>  %PARRDR-ERROR: duplication of nonbonded entry C_8
>  %PARRDR-ERROR: duplication of nonbonded entry C_10
>  %PARRDR-ERROR: duplication of nonbonded entry C_12
>
> usually this kind of error message of duplication comes when we give some
> coordinates second time.an error message "duplicating the atom " appears.
> but in the parameter file it is showing this error message.
>
> and one more problem i am facing.i could run cns successfully except the
> above mentioned error.but in the electron density map i am seeing the fofc
> density (along with 2fofc) for the three chlorines in triclosan where as
> the rest of the molecule is in 2fofc alone. what are the other parameters
> that i need to check to get out of this problem.at contour level 5 for
> fofc only i am getting rid of the fofc density. is it because chlorine
> contains more no of electrons than carbon, nitrogen and oxygen. my cns is
> taking all the atoms ie., number of atoms is matching. have anybody faced
> such problem while fitting any heavy atoms or ligands with more electrons.
>
> plz guide me how to proceed.
>
>
> P.Lakshmi Swarna Mukhi,
> Prof.KSuguna's lab,
> Molecular BIophysics Unit,
> Indian Institute of Science,
> Bangalore -560012
>
>
>
>


##############################################################################

Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava@davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

        O     C           O     C         Visit the PRODRG server to take
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "
       O