Sorry, but I've nowhere else to turn, I hope nobody minds. In trying to model a nonyl glucoside ligand into my model, I get the following errors when trying to run the refine.inp script:
%NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%% ATOM: SEGId=" ", RESId="2077", NAME="C1 ", CHEMical="C_1 " %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%% ATOM: SEGId=" ", RESId="2077", NAME="C6 ", CHEMical="C_6 " %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%% ATOM: SEGId=" ", RESId="2077", NAME="C9' ", CHEMical="C_15" %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%% ATOM: SEGId=" ", RESId="2077", NAME="O2 ", CHEMical="O_17" %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%% ATOM: SEGId=" ", RESId="2077", NAME="O3 ", CHEMical="O_18" %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%% ATOM: SEGId=" ", RESId="2077", NAME="O4 ", CHEMical="O_19" %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%% ATOM: SEGId=" ", RESId="2077", NAME="O5 ", CHEMical="O_20" %NBUPDA-ERR: missing nonbonded Lennard-Jones parameters %%%%%%% ATOM: SEGId=" ", RESId="2077", NAME="O6 ", CHEMical="O_21" %NBUPDA error encountered: program will be aborted. (CNS is in mode: SET ABORT=NORMal END) ***************************************************** ABORT mode will terminate program execution. ***************************************************** Program will stop immediately. as I understand it this has something to do with O renumbering the ligand after one fits it and has O write the coordinates out and that the new coordinates don't match up to the NONBonded lists in the .par file, however, as a test, I get this error AFTER I downloaded the file from Hic-Up, attached it to my generate.inp into file, ran the script, and then used the output from the generate.inp script as input for the refine.inp script - so there was no possibility for O to muck things up. Anyway, it's funny in that it's only 8 of 21 atoms that seem to exhibit this problem and not the whole mess. Does anyone have any ideas? thanks a lot, Jon Caruthers
