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

["P. LAKSHMI SWARNA MUKHI" <plsmukhi@mbu.iisc.ernet.in>]

***  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