Hi Mark-- > > I tried both approaches (1) wrefine_Zn.py & (2) wrefine_Zn_cs.py > (below), but both give what might be the same error (with the errors > at the bottom)
> %CODBON-ERR: missing bond parameters %%%%%%%%%%%%%%%%%%%%%%%%%% > bond energy constant missing. > target bond length missing. > ATOM1: SEGId=" ", RESId="401 ", NAME="ZN+2", CHEMical="ZN+2" > ATOM2: SEGId=" ", RESId="6 ", NAME="SG ", CHEMical="SH1E" Sorry- the zinc finger parameter file works with the default Xplor-NIH parameters. For water refinement, different chemical types are required. Please take the attached file and place it in your calculation directory. ######################################################################## To unsubscribe from the XPLOR-NIH list, click the following link: http://list.nih.gov/cgi-bin/wa.exe?SUBED1=XPLOR-NIH&A=1
zn-finger-allhdg5.3.par
Description: Binary data
Then, replace the line
protocol.initParams('extra/zn-finger.par')
with
protocol.initParams('zn-finger-allhdg5.3.par')
I have not tested this- please let me know of you have difficulties.
Charles
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