Hi Jonathan,
try using the PRODRG Server with your coordinates, or alternatively
run Refmac reading in the cif file for your ligand.
Jürgen
On 3 Oct 2008, at 14:25, Jonathan Marvin Caruthers wrote:
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
-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 98195
Box 357742
Phone: +1-206-616-4510
FAX: +1-206-685-7002
Web: http://faculty.washington.edu/jbosch
