Re: [ccp4bb] parameter and topology files in CNS

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

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

Next message:
Subject: Re: parameter and topology files in CNS
From: Raji Edayathumangalam redayath {- at -} MAIL {- dot -} ROCKEFELLER {- dot -} EDU
Date: 2007-06-25

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

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

Next message:
Subject: Re: parameter and topology files in CNS
From: Raji Edayathumangalam redayath {- at -} MAIL {- dot -} ROCKEFELLER {- dot -} EDU
Date: 2007-06-25