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

[Jayasankar Jasti <ccp4in@yahoo.com>]

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Hi!

i think this problem comes when generating topology
and parameter files manually and specifying same
unique letter for several ligands..

jayasankar

--- Daan Virtual <vdava@davapc1.bioch.dundee.ac.uk>
wrote:
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> 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
> 


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