Dear Amber users,
My protein has two Cys4-Zn, so I used MCPB to generate ZAFF.frcmod and
ZAFF.prepi (see below). Then I loaded these two files into leap, and then
load my protein. But the ZN is still not recognized and I got "Unknown
residue: ZN number: 74 type: Terminal/beginning
..relaxing end constraints to try for a dbase match-no luck". Did I miss
anything? Anyone can help me with this? Thank you very much.
*MCPB -i mcpb.bcl -l mcpb.log*
*mcpb.bcl*
*set AMBERHOME $AMBERHOME*
*loadParam AMBERHOME/dat/mtkpp/parm94.xmlloadParam
AMBERHOME/dat/mtkpp/parm_gaff.xml loadParam
AMBERHOME/dat/mtkpp/metals/metalParm.xml*
*loadParam AMBERHOME/dat/mtkpp/ZAFF/ZAFF_parm.xmlwriteFrcmodFile
ZAFF.frcmod ZAFF*
*loadLib AMBERHOME/dat/mtkpp/ZAFF/ZAFF.xmlwritePrepFile ZAFF.prepi Zn-CCCC*
*quit*
Regards,
Nadia
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Received on Thu Jul 31 2014 - 10:00:02 PDT
