Re: [ccp4bb]: Solvent building w/ ArpWarp

[sameeta bilgrami <sameeta_b@yahoo.co.in>]

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 --- Tristan Fiedler <tfiedler@newssun.med.miami.edu>
wrote: > Dear CCP4 users,
> 
> We are testing ArpWarp v. 5.1 mode solvent for our
> initial placement of
> water molecules.
> 
> The program calls CCP4 programs [protin, refmac],
> however errors are
> resulting due to incorrectly defined atom and
> residue names.  Where can
> one find the accepted names for atoms/residues
> accepted by the CCP4
> suite of programs, analogous to the
> topology/parameter files in
> XPLOR/CNS or the stereochem/refidict/connectivity -
> type files for O.
> 
> A sample of the errors is listed below.
> 
> Thank you for your tips!
> 
> tristan fiedler
> 
> 
> 
> 
> ***ERROR:  Group Name MSE   given for Residue No. 
> 14
>    is NOT among those in the table of standard
> groups.
> 
> **** ERROR ****
>  Atom Name OT1  Given for Residue No. xxx
>    is not among those in the standard table for the
> LEUC Group.  ATOM
> OMITTED.
>  **** ERROR ****
>  Atom Name OT2  Given for Residue No. xxx
>    is not among those in the standard table for the
> LEUC Group.  ATOM
> OMITTED.
> 
> .....
> O    of LEUC 180
>  OT   of LEUC 180
>  OE   of LEUC 180
>  OXT  of LEUC 180
>  O    of LEUC 180
>  OT   of LEUC 180
>  OE   of LEUC 180
>  OXT  of LEUC 180
>  O    of LEUC 180
>  OT   of LEUC 180
>  OE   of LEUC 180
>  OXT  of LEUC 180
>  O    of LEUC 180
>  OT   of LEUC 180
>  OE   of LEUC 180
>  OXT  of LEUC 180
> 
> 
> 
> --
> Tristan J. Fiedler, Ph.D.
> 
> Malhotra Laboratory
> Department of Biochemistry & Molecular Biology
> University of Miami Medical School
> 
> tfiedler@newssun.med.miami.edu
> 
> hi!,
     i think the problem is the OXt that is put by the
cns ..just remove it and run ..i think it should run
.....all the definitions of residues etc are in a file
called protin.dic .....sameeta
>  

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