We are testing ArpWarp v. 5.1 mode solvent for our initial placement of water molecules.
The program calls CCP4 programs [protin, refmac], however errors are resulting due to incorrectly defined atom and residue names. Where can one find the accepted names for atoms/residues accepted by the CCP4 suite of programs, analogous to the topology/parameter files in XPLOR/CNS or the stereochem/refidict/connectivity - type files for O.
A sample of the errors is listed below.
Thank you for your tips!
tristan fiedler
***ERROR: Group Name MSE given for Residue No.
14
is NOT among those in the table of standard groups.
**** ERROR ****
Atom Name OT1 Given for Residue No. xxx
is not among those in the standard table for the LEUC
Group. ATOM OMITTED.
**** ERROR ****
Atom Name OT2 Given for Residue No. xxx
is not among those in the standard table for the LEUC
Group. ATOM OMITTED.
...
O of LEUC 180
OT of LEUC 180
OE of LEUC 180
OXT of LEUC 180
O of LEUC 180
OT of LEUC 180
OE of LEUC 180
OXT of LEUC 180
O of LEUC 180
OT of LEUC 180
OE of LEUC 180
OXT of LEUC 180
O of LEUC 180
OT of LEUC 180
OE of LEUC 180
OXT of LEUC 180
-- Tristan J. Fiedler, Ph.D.
Malhotra Laboratory Department of Biochemistry & Molecular Biology University of Miami Medical School tfiedler@newssun.med.miami.edu