Hello all,
I have been having major issues with CNS that I havent been able to figure out.
My protein has 2 molecules in the asu, ds DNA, ions, and a ligand. I have been
using refmac for refinement but need to make a composite omit map so that I can
check things out in CNS.
here is the problem
every time I run generate.inp I get errors like this in the logfile
COOR>HETATM 3389 NA NA E 1 -4.719 7.010 17.729 1.00 33.51
NA
SEGMNT: 3 residues were inserted into segment " "
CHAIN> end
SEGMENT> if ( &ion_rename_$counter = true ) then
%SEGMENT-ERR: unrecognized command:
if
^^
%SEGMENT-ERR: unrecognized command:
if (
^
%SEGMENT-ERR: unrecognized command:
if ( false
^^^^^
%SEGMENT-ERR: unrecognized command:
if ( false =
^
%SEGMENT-ERR: unrecognized command:
if ( false = true
^^^^
%SEGMENT-ERR: unrecognized command:
if ( false = true )
^
%SEGMENT-ERR: unrecognized command:
if ( false = true ) then
^^^^
SEGMENT> do (refy=$counter) (attr refx=9999)
%SEGMENT-ERR: unrecognized command:
do
^^
%SEGMENT-ERR: unrecognized command:
do (r
^
%SEGMENT-ERR: unrecognized command:
do (refy=
^^^^
%SEGMENT-ERR: unrecognized command:
do (refy=$
^
%SEGMENT-ERR: unrecognized command:
do (refy=$counter)
^^^^^^^^
%PARSER error encountered: Encountered too many parsing errors.
(CNS is in mode: SET ABORT=NORMal END)
I have changed all of my files so that CNS will like them. (outputs from coot
are not liked by cns) I changed the dna using fix_dna_rna indna > outdna. and
manually changed the c5m for thymine to c5a for cns. Also made sure the sugar
ring atoms had (') and not (*). I also changed the CD1 ILE to CD ILE because
CNS hates CD1 ILE for some reason. One of my ligands is funny so I downloaded
the topology and parameter files from HIcCup and put them in the necessary
sections in generate.inp. I have run this before when refining a similar data
set with not as many issues, but I really would like to know what this means.
thanks all
Ainsley
C. Ainsley Davis, Ph.D.
Post-Doctoral Fellow
Massachusetts Institute of Technology
Department of Chemistry 56-546
32 Vassar Street
Cambridge, MA 02142
Phone Number: (617) 258-7021
Fax Number: (617) 258-7847
E-mail: [EMAIL PROTECTED]
