[ccp4bb] parameter and topology files in CNS

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Fedora core 6 install problem
From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-06-25

Next message:
Subject: Re: parameter and topology files in CNS
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-06-25

Subject: parameter and topology files in CNS
From: Jae Hyun jaehyun {- dot -} bae {- at -} YALE {- dot -} EDU
Date: 2007-06-25

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

Refmac_5.2.0019: New ligand has been encountered. Stopping now
Times: User: 7.7s System: 0.2s Elapsed: 0:08

I need your kind advice to solve this problem. Thank you in adveance.

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Fedora core 6 install problem
From: Roger Rowlett RRowlett {- at -} MAIL {- dot -} COLGATE {- dot -} EDU
Date: 2007-06-25

Next message:
Subject: Re: parameter and topology files in CNS
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-06-25