Hi Jae, Try resetting the MAXJNT parameter (increase the set value). I had problems with MAXA and other parameters and I suspect your problem has the same solution. You might need root access for the same.
Also, make sure that you are specifically asking to read the topology and parameter files in the CNS 'generate' and 'minimize' input files. Hope that helps. Raji ---------Included Message---------- >Try elbow.builder and phenix.refine in the phenix package. It will make >your life much easier. > > >Jae Hyun wrote: >> Dear all, >> >> I have a decavanadate anion in my structure, and want to refine it. For >> that, I got parameter and topology files from HIC-Up website, and used in >> CNS. But, it gave the error message as follows: >> >> Program version= 1.1 File version= 1.1 >> Torsion Topology> >> Torsion Topology> fix group ( &atom_rigid ) >> SELRPN: 0 atoms have been selected out of 4464 >> Torsion Topology> >> Torsion Topology> end >> Torsion Dynamics> nstep=0 >> Torsion Dynamics> cmremove=true >> Torsion Dynamics> end >> -------------------------- Torsion Topology >> ----------------------------------- >> ERROR: A group has too many joints. >> Please increase MAXJNT and re-run. >> >> %TORSION:TOPOLOGY error encountered: Fatal Topology Error >> (CNS is in mode: SET ABORT=NORMal END) >> ***************************************************** >> ABORT mode will terminate program execution. >> ***************************************************** >> Program will stop immediately. >> >> >> And, I also tried to generate CIF files of the decavanadate so that I can >> use REFMAC. But, it gives other error message like this: >> >> >> WARNING : DVT : observed angle value will used >> chem_type : OH1 -V -O 99.322 (O26 -V9 -O8 >> WARNING : DVT : observed angle value will used >> chem_type : O2 -V -O 79.829 (O4 -V9 -O8 >> WARNING : DVT : observed angle value will used >> chem_type : O2 -V -O 152.442 (O27 -V9 -O8 >> WARNING : DVT : observed angle value will used >> chem_type : O2 -V -OH1 99.366 (O23 -V10 -O28 >> WARNING : DVT : observed angle value will used >> chem_type : O2 -V -O2 78.183 (O23 -V10 -O18 >> WARNING : DVT : observed angle value will used >> chem_type : O2 -V -O2 154.744 (O23 -V10 -O15 >> WARNING : DVT : observed angle value will used >> chem_type : O2 -V -O2 75.004 (O23 -V10 -O27 >> WARNING : DVT : observed angle value will used >> chem_type : O2 -V -O 75.164 (O23 -V10 -O2 >> WARNING : DVT : observed angle value will used >> chem_type : O2 -V -O2 99.544 (O18 -V10 -O15 >> WARNING : DVT : observed angle value will used >> chem_type : O2 -V -O2 147.025 (O18 -V10 -O27 >> WARNING : DVT : observed angle value will used >> chem_type : O2 -V -O2 96.632 (O15 -V10 -O27 >> WARNING : DVT : observed angle value will used >> chem_type : O2 -V -O 79.049 (O18 -V10 -O2 >> WARNING : DVT : observed angle value will used >> chem_type : O2 -V -O 79.699 (O15 -V10 -O2 >> WARNING : DVT : observed angle value will used >> chem_type : O2 -V -O 75.832 (O27 -V10 -O2 >> WARNING : DVT : observed angle value will used >> chem_type : OH1 -V -O2 102.115 (O28 -V10 -O18 >> WARNING : DVT : observed angle value will used >> chem_type : OH1 -V -O2 105.654 (O28 -V10 -O15 >> WARNING : DVT : observed angle value will used >> chem_type : OH1 -V -O2 100.876 (O28 -V10 -O27 >> WARNING : DVT : observed angle value will used >> chem_type : OH1 -V -O 174.132 (O28 -V10 -O2 >> WARNING: there is not metal chirality for:V10 >> WARNING: there is not metal chirality for:V1 >> WARNING: there is not metal chirality for:V9 >> WARNING: there is not metal chirality for:V7 >> WARNING: there is not metal chirality for:V6 >> WARNING: there is not metal chirality for:V8 >> WARNING: there is not metal chirality for:V5 >> WARNING: there is not metal chirality for:V2 >> WARNING: there is not metal chirality for:V4 >> WARNING: there is not metal chirality for:V3 >> * Plotfile: /tmp/refmac5_temp1.20489_new_DVT.ps >> -------------------------------- >> --- title of input coord file --- >> >> PDB_code:xxxx >> PDB_name:---- >> PDB_date:XX-XXX-XX >> -------------------------------- >> ... and more ... >> Number of chains : 4 >> Total number of monomers : 624 >> Number of atoms : 4430 >> Number of missing atoms : 71 >> Number of rebuilt atoms : 0 >> Number of unknown atoms : 0 >> Number of deleted atoms : 0 >> >> Number of bonds restraints : 4389 >> Number of angles restraints : 6074 >> Number of torsions restraints : 3037 >> Number of chiralities : 638 >> Number of planar groups : 763 >> I am writing new library: >> /ccp4/P >> >> Important, Important, Important!!!!! >> >> Your coordinate file has a ligand which has either minimum or no >> description >> in the library >> A new ligand description has been added to /ccp4/PROJECT_6_lib.cif >> Picture of the new ligand can be viewed using postscript file. See above >> Check description in this file and, if satisfied, use it as the input >> library >> Otherwise either edit bond orders manually or use CCP4i Sketcher to view >> and >> edit the ligand >> and create a library entry by running libcheck >> It is strongly recommended that dictionary entry should be checked >> carefully before using it >> If you are happy with the library description then use the keyword (MAKE >> CHECK NONE) >> I.e. do not check correctness of the coordinates >> ===> Error: New ligand has been encountered. Stopping now >> <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> >> Refmac_5.2.0019: New ligand has been encountered. Stopping now >> Times: User: 7.7s System: 0.2s Elapsed: 0:08 >> </pre> >> </html> >> <!--SUMMARY_END--></FONT></B> >> >> >> I need your kind advice to solve this problem. Thank you in adveance. >> > ---------End of Included Message----------
