The sizes of several arrays (such as the ones that store atomic positions) are
defined at compile time, and your structure appears to have run up against one
such limit. Here's what the CNS website says:
"Changing array dimensions
The array dimensions for several arrays which may need to be changed (e.g. the
maximum number of atoms) are defined at compile time in the include file
$CNS_SOLVE/source/cns.inc. Modify this file then recompile CNSsolve using make
cns_solve."
Josh
Quoting Sampath Natarajan <[log in to unmask]>:
> Dear all,
> I have some problem while creating the structural topology files for
> CNS refinement. In the log file I find that the error message like
> ?%GENRES error encountered: exceeded MAXB parameter --> recompile program?
>
> I don?t understand the problem. All suggestions are welcome for this
> problem. I?m giving here the output log file for your kind attention.
> Thanks in advance.
>
> Yours sincerely,
> Sampath
> ============================================================
> | |
> | Crystallography & NMR System (CNS) |
> | CNSsolve |
> | |
> ============================================================
> Version: 1.1
> Status: General release
> ============================================================
> Written by: A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano,
> P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang,
> J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read,
> L.M.Rice, T.Simonson, G.L.Warren.
> Copyright (c) 1997-2001 Yale University
> ============================================================
> Running on machine: xray.skku.ac.kr (Unix-g77,32-bit)
> Program started by: sam
> Program started at: 15:08:11 on 23-Aug-2007
> ============================================================
>
> FFT3C: Using FFTPACK4.1
>
> CNSsolve>{+ file: generate_easy.inp +}
> CNSsolve>{+ directory: general +}
> CNSsolve>{+ description: Generate coordinate and structure file for
> simple models +}
> CNSsolve>{+ comment:
> CNSsolve> This is designed to be a means of generating a coordinate
> CNSsolve> and structure file for commonly encountered
> models: protein
> CNSsolve> and/or DNA/RNA plus waters and maybe ligands. The
> coordinates
> CNSsolve> are provided by the user in a single input PDB file.
> CNSsolve> Disulphide bonds will be automatically determined
> by distance.
> CNSsolve> If required generate hydrogens. Any atoms with unknown
> CNSsolve> coordinates can be automatically generated +}
> CNSsolve>{+ authors: Paul Adams and Axel Brunger +}
> CNSsolve>{+ copyright: Yale University +}
> CNSsolve>
> CNSsolve>{- Guidelines for using this file:
> CNSsolve> - all strings must be quoted by double-quotes
> CNSsolve> - logical variables (true/false) are not quoted
> CNSsolve> - do not remove any evaluate statements from the file -}
> CNSsolve>
> CNSsolve>{- Special patches will have to be entered manually at the
> relevant points
> CNSsolve> in the file - see comments throughout the file -}
> CNSsolve>
> CNSsolve>{- begin block parameter definition -} define(
> DEFINE>
> DEFINE>{============================== important
> =================================}
> DEFINE>
> DEFINE>{* Different chains in the structure must have either unique segid or
> DEFINE> chainid records. If this is no the case, the end of a chain must
> DEFINE> be delimited by a TER card. *}
> DEFINE>
> DEFINE>{* A break in a chain can be detected automatically or should
> be delimited
> DEFINE> by a BREAK card. In this case no patch (head, tail or link) will be
> DEFINE> applied between the residues that bound the chain break. *}
> DEFINE>
> DEFINE>{* NB. The input PDB file must finish with an END statement *}
> DEFINE>
> DEFINE>{=========================== coordinate files
> =============================}
> DEFINE>
> DEFINE>{* coordinate file *}
> DEFINE>{===>} coordinate_infile="Amore.pdb";
> DEFINE>
> DEFINE>{* convert chainid to segid if chainid is non-blank *}
> DEFINE>{+ choice: true false +}
> DEFINE>{===>} convert=true;
> DEFINE>
> DEFINE>{* separate chains by segid - a new segid starts a new chain *}
> DEFINE>{+ choice: true false +}
> DEFINE>{===>} separate=true;
> DEFINE>
> DEFINE>{============================ renaming atoms
> ===============================}
> DEFINE>
> DEFINE>{* some atoms may need to be renamed in the topology database
> to conform
> DEFINE> to what is present in the coordinate file *}
> DEFINE>
> DEFINE>{* delta carbon in isoleucine is named CD in CNS
> DEFINE> what is it currently called in the coordinate file? *}
> DEFINE>{* this will not be changed if left blank *}
> DEFINE>{===>} ile_CD_becomes="CD1";
> DEFINE>
> DEFINE>{* terminal oxygens are named OT1 and OT2 in CNS
> DEFINE> what are they currently called in the coordinate file? *}
> DEFINE>{* these will not be changed if left blank *}
> DEFINE>{===>} OT1_becomes="O";
> DEFINE>{===>} OT2_becomes="OXT";
> DEFINE>
> DEFINE>{======================= automatic mainchain breaks
> ========================}
> DEFINE>
> DEFINE>{* automatically detect mainchain breaks in proteins based on
> distance *}
> DEFINE>{* the peptide link at break points will be removed *}
> DEFINE>{+ choice: true false +}
> DEFINE>{===>} auto_break=true;
> DEFINE>
> DEFINE>{* cutoff distance in Angstroms for identification of breaks *}
> DEFINE>{* the default of 2.5A should be reasonable for most cases. If
> the input
> DEFINE> structure has bad geometry it may be necessary to increase
> this distance *}
> DEFINE>{===>} break_cutoff=2.5;
> DEFINE>
> DEFINE>{* file containing patches to delete peptide links *}
> DEFINE>{===>} prot_break_infile="CNS_TOPPAR:protein_break.top";
> DEFINE>
> DEFINE>{======================= automatic disulphide bonds
> ========================}
> DEFINE>
> DEFINE>{* cutoff distance in Angstroms for identification of disulphides *}
> DEFINE>{* the default of 3.0A should be reasonable for most cases. If
> the input
> DEFINE> structure has bad geometry it may be necessary to increase
> this distance *}
> DEFINE>{===>} disulphide_dist=3.0;
> DEFINE>
> DEFINE>{========================= RNA to DNA conversion
> ==========================}
> DEFINE>
> DEFINE>{* All nucleic acid residues initially have ribose sugars (rather than
> DEFINE> deoxyribose). A patch must be applied to convert the ribose
> to deoxyribose
> DEFINE> for DNA residues. Select those residues which need to have
> the patch
> DEFINE> applied to make them DNA. *}
> DEFINE>{* Make sure that the atom selection is specific for the nucleic acid
> DEFINE> residues *}
> DEFINE>{===>} dna_sele=(none);
> DEFINE>
> DEFINE>{========================= generate parameters
> =============================}
> DEFINE>
> DEFINE>{* hydrogen flag - determines whether hydrogens will be output *}
> DEFINE>{* must be true for NMR, atomic resolution X-ray crystallography
> DEFINE> or modelling. Set to false for most X-ray crystallographic
> DEFINE> applications at resolution > 1A *}
> DEFINE>{+ choice: true false +}
> DEFINE>{===>} hydrogen_flag=false;
> DEFINE>
> DEFINE>{* which hydrogens to build *}
> DEFINE>{+ choice: "all" "unknown" +}
> DEFINE>{===>} hydrogen_build="all";
> DEFINE>
> DEFINE>{* selection of atoms other than hydrogens for which coordinates
> DEFINE> will be generated *}
> DEFINE>{* to generate coordinates for all unknown atoms use: (not(known)) *}
> DEFINE>{===>} atom_build=(not(known));
> DEFINE>
> DEFINE>{* selection of atoms to be deleted *}
> DEFINE>{* to delete no atoms use: (none) *}
> DEFINE>{===>} atom_delete=(none);
> DEFINE>
> DEFINE>{* set bfactor flag *}
> DEFINE>{+ choice: true false +}
> DEFINE>{===>} set_bfactor=false;
> DEFINE>
> DEFINE>{* set bfactor value *}
> DEFINE>{===>} bfactor=15.0;
> DEFINE>
> DEFINE>{* set occupancy flag *}
> DEFINE>{+ choice: true false +}
> DEFINE>{===>} set_occupancy=false;
> DEFINE>
> DEFINE>{* set occupancy value *}
> DEFINE>{===>} occupancy=1.0;
> DEFINE>
> DEFINE>{============================= output files
> ================================}
> DEFINE>
> DEFINE>{* output structure file *}
> DEFINE>{===>} structure_outfile="m18.mtf";
> DEFINE>
> DEFINE>{* output coordinate file *}
> DEFINE>{===>} coordinate_outfile="m18.pdb";
> DEFINE>
> DEFINE>{* format output coordinates for use in o *}
> DEFINE>{* if false then the default CNS output coordinate format will
> be used *}
> DEFINE>{+ choice: true false +}
> DEFINE>{===>} pdb_o_format=true;
> DEFINE>
> DEFINE>{================== protein topology and parameter files
> ===================}
> DEFINE>
> DEFINE>{* protein topology file *}
> DEFINE>{===>} prot_topology_infile="CNS_TOPPAR:protein.top";
> DEFINE>
> DEFINE>{* protein linkage file *}
> DEFINE>{===>} prot_link_infile="CNS_TOPPAR:protein.link";
> DEFINE>
> DEFINE>{* protein parameter file *}
> DEFINE>{===>} prot_parameter_infile="CNS_TOPPAR:protein_rep.param";
> DEFINE>
> DEFINE>{================ nucleic acid topology and parameter files
> =================}
> DEFINE>
> DEFINE>{* nucleic acid topology file *}
> DEFINE>{===>} nucl_topology_infile="CNS_TOPPAR:dna-rna.top";
> DEFINE>
> DEFINE>{* nucleic acid linkage file *}
> DEFINE>{* use CNS_TOPPAR:dna-rna-pho.link for 5'-phosphate *}
> DEFINE>{===>} nucl_link_infile="CNS_TOPPAR:dna-rna.link";
> DEFINE>
> DEFINE>{* nucleic acid parameter file *}
> DEFINE>{===>} nucl_parameter_infile="CNS_TOPPAR:dna-rna_rep.param";
> DEFINE>
> DEFINE>{=================== water topology and parameter files
> ====================}
> DEFINE>
> DEFINE>{* water topology file *}
> DEFINE>{===>} water_topology_infile="CNS_TOPPAR:water.top";
> DEFINE>
> DEFINE>{* water parameter file *}
> DEFINE>{===>} water_parameter_infile="CNS_TOPPAR:water_rep.param";
> DEFINE>
> DEFINE>{================= carbohydrate topology and parameter files
> ===============}
> DEFINE>
> DEFINE>{* carbohydrate topology file *}
> DEFINE>{===>} carbo_topology_infile="CNS_TOPPAR:carbohydrate.top";
> DEFINE>
> DEFINE>{* carbohydrate parameter file *}
> DEFINE>{===>} carbo_parameter_infile="CNS_TOPPAR:carbohydrate.param";
> DEFINE>
> DEFINE>{============= prosthetic group topology and parameter files
> ===============}
> DEFINE>
> DEFINE>{* prosthetic group topology file *}
> DEFINE>{===>} prost_topology_infile="";
> DEFINE>
> DEFINE>{* prosthetic group parameter file *}
> DEFINE>{===>} prost_parameter_infile="";
> DEFINE>
> DEFINE>{=================== ligand topology and parameter files
> ===================}
> DEFINE>
> DEFINE>{* ligand topology file *}
> DEFINE>{===>} ligand_topology_infile="";
> DEFINE>
> DEFINE>{* ligand parameter file *}
> DEFINE>{===>} ligand_parameter_infile="";
> DEFINE>
> DEFINE>{===================== ion topology and parameter files
> ====================}
> DEFINE>
> DEFINE>{* ion topology file *}
> DEFINE>{===>} ion_topology_infile="CNS_TOPPAR:ion.top";
> DEFINE>
> DEFINE>{* ion parameter file *}
> DEFINE>{===>} ion_parameter_infile="CNS_TOPPAR:ion.param";
> DEFINE>
> DEFINE>{===========================================================================}
> DEFINE>{ things below this line do not need to be changed
> }
> DEFINE>{===========================================================================}
> DEFINE>
> DEFINE> ) {- end block parameter definition -}
> CNSsolve>
> CNSsolve> checkversion 1.1
> Program version= 1.1 File version= 1.1
> CNSsolve>
> CNSsolve> evaluate ($log_level=quiet)
> Assuming literal string "QUIET"
> EVALUATE: symbol $LOG_LEVEL set to "QUIET" (string)
> CNSsolve>
> CNSsolve> topology
> RTFRDR> if ( &BLANK%prot_topology_infile = false ) then
> NEXTCD: condition evaluated as true
> RTFRDR> @@&prot_topology_infile
> ASSFIL: file
> /usr/local/cns/cns_solve_1.1/libraries/toppar/protein.top opened.
> RTFRDR>remarks file toppar/protein.top
> RTFRDR>remarks protein topology for crystallographic structure
> determination
> RTFRDR>
> RTFRDR>!
> RTFRDR>! Please cite the following reference when using these parameters:
> RTFRDR>! Engh, R.A. and Huber, R. (1991). Accurate Bond and
> RTFRDR>! Angle Parameters for X-ray Protein-Structure Refinement,
> RTFRDR>! Acta Cryst. A47, 392-400.
> RTFRDR>!
> RTFRDR>!
> RTFRDR>
> RTFRDR>set echo=false end
> Program version= 1.1 File version= 1.1
> RTFRDR>
> RTFRDR> end if
> RTFRDR> if ( &BLANK%nucl_topology_infile = false ) then
> NEXTCD: condition evaluated as true
> RTFRDR> @@&nucl_topology_infile
> ASSFIL: file
> /usr/local/cns/cns_solve_1.1/libraries/toppar/dna-rna.top opened.
> RTFRDR>remarks file toppar/dna-rna.top
> RTFRDR>remarks dna/rna topology for crystallographic structure
> determination
> RTFRDR>
> RTFRDR>! removed references to CA, CF, CS, MG, NH3, OS (ATB 12/30/94)
> RTFRDR>! removed TIP3 water model (ATB 12/30/94)
> RTFRDR>! mapped NA->NNA, CH3E->CC3E (ATB 12/30/94)
> RTFRDR>
> RTFRDR>!
> RTFRDR>!Please cite the following reference when using these parameters:
> RTFRDR>!G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman,
> RTFRDR>! New Parameters for the Refinement of Nucleic Acid
> Containing Structures,
> RTFRDR>! Acta Cryst. D, 52, 57-64 (1996).
> RTFRDR>!
> RTFRDR>! Oct. 8, 1996 - Modified by Alexey Bochkarev (McMaster University)
> RTFRDR>! to process properly 5PHO (5'-terminus with
> phosphate) patch.
> RTFRDR>! Geometry and charges of -O5'-PO3 group were
> taken from
> RTFRDR>! Saenger W. 1984. Principles of Nucleic Acid
> Structure
> RTFRDR>! All modifications are placed between:
> RTFRDR>!***AB***
> RTFRDR>!....included fragment
> RTFRDR>!***AB end***
> RTFRDR>! New atomic types were introduced to describe
> RTFRDR>! -O5'-PO3 group: O5H (O5') O1PH (O1P) O2PH (O2P)
> RTFRDR>! in addition to existing OH (O5T)
> RTFRDR>
> RTFRDR>set echo=false end
> Program version= 1.1 File version= 1.1
> RTFRDR>
> RTFRDR> end if
> RTFRDR> if ( &BLANK%water_topology_infile = false ) then
> NEXTCD: condition evaluated as true
> RTFRDR> @@&water_topology_infile
> ASSFIL: file /usr/local/cns/cns_solve_1.1/libraries/toppar/water.top opened.
> RTFRDR>remarks file toppar/water.top
> RTFRDR>remarks water topology for crystallographic structure determination
> RTFRDR>remarks based on Jorgensen Tip3p water model
> RTFRDR>
> RTFRDR>set echo=false end
> Program version= 1.1 File version= 1.1
> RTFRDR> end if
> RTFRDR> if ( &BLANK%carbo_topology_infile = false ) then
> NEXTCD: condition evaluated as true
> RTFRDR> @@&carbo_topology_infile
> ASSFIL: file
> /usr/local/cns/cns_solve_1.1/libraries/toppar/carbohydrate.top opened.
> RTFRDR>REMARKS toppar/carbohydrate.top {pyranose sugar toplogoy for
> crystallographic
> RTFRDR>remarks structure determination}
> RTFRDR>REMARKS FOR USE WITH CARBOHYDRATE.PARAM AND protein_rep.param
> PROTEIN PARAMETERS
> RTFRDR>REMARKS ==========================================================
> RTFRDR>REMARKS Bill Weis 10-July-1988
> RTFRDR>REMARKS Also see CARBOHYDRATE.PARAM for parameters.
> RTFRDR>REMARKS Charges taken from John Brady's glucose topology file
> for ring,
> RTFRDR>REMARKS others from protein parameter file.
> RTFRDR>REMARKS Idealized values for impropers at ring carbons to allow simple
> RTFRDR>REMARKS construction of various anomers/epimers.
> RTFRDR>REMARKS Any other hexose or link can be easily constructed by
> analogy to these.
> RTFRDR>
> RTFRDR>REMARKS Additions 6-March-1992 Bill Weis for use with PARAM2.CHO
> RTFRDR>REMARKS New atom types CCA, CCE, OA for the C1 & O1 positions
> to account
> RTFRDR>REMARKS for different bond and angle values due to the
> anomeric effect.
> RTFRDR>REMARKS More accurate equilibrium values for bond angle around
> this oxygen
> RTFRDR>REMARKS in glycosidic linkages. CCE for equatorial O1, CCA for
> RTFRDR>REMAKRS axial O1. For free sugar, keep OH1 as O1 atomtype;
> changed to OA
> RTFRDR>REMARKS for linkages.
> RTFRDR>REMARKS References: G.A. Jeffrey (1990) Acta Cryst B46, 89-103;
> RTFRDR>REMARKS K. Hirotsu & A.Shimada, (1974) Bull. Chem. Soc. Japan,
> 47, 1872-1879.
> RTFRDR>
> RTFRDR>REMARKS Additional CC6 atomtype for exocyclic carbon 5/11/92
> RTFRDR>
> RTFRDR>set echo=false end
> Program version= 1.1 File version= 1.1
> RTFRDR>
> RTFRDR> end if
> RTFRDR> if ( &BLANK%prost_topology_infile = false ) then
> NEXTCD: condition evaluated as false
> RTFRDR> @@&prost_topology_infile
> RTFRDR> end if
> RTFRDR> if ( &BLANK%ligand_topology_infile = false ) then
> NEXTCD: condition evaluated as false
> RTFRDR> @@&ligand_topology_infile
> RTFRDR> end if
> RTFRDR> if ( &BLANK%ion_topology_infile = false ) then
> NEXTCD: condition evaluated as true
> RTFRDR> @@&ion_topology_infile
> ASSFIL: file /usr/local/cns/cns_solve_1.1/libraries/toppar/ion.top opened.
> RTFRDR>remarks file toppar/ion.top
> RTFRDR>remarks topology and masses for common ions
> RTFRDR>remarks Dingle atom ion residues are given the name of the element.
> RTFRDR>remarks By default the atom will be uncharged (eg. the residue MG will
> RTFRDR>remarks contain the atom called MG with zero charge).
> RTFRDR>remarks To use the charged species the charge state is appended to
> RTFRDR>remarks the atom name (eg to use MG2+ the residue name is MG2, and the
> RTFRDR>remarks atom name is MG+2 and has charge +2.0).
> RTFRDR>remarks NOTE: not all ionic species are represented
> RTFRDR>remarks PDA 02/09/99
> RTFRDR>
> RTFRDR>set echo=false end
> Program version= 1.1 File version= 1.1
> RTFRDR> end if
> RTFRDR> end
> CNSsolve>
> CNSsolve> topology
> RTFRDR> if ( &BLANK%prot_break_infile = false ) then
> NEXTCD: condition evaluated as true
> RTFRDR> @@&prot_break_infile
> ASSFIL: file
> /usr/local/cns/cns_solve_1.1/libraries/toppar/protein_break.top
> opened.
> RTFRDR>remarks file toppar/protein_break.top
> RTFRDR>remarks patches to remove peptide linkages
> RTFRDR>
> RTFRDR>! Paul Adams 28th June 1999
> RTFRDR>! Yale University
> RTFRDR>
> RTFRDR>set echo=false end
> Program version= 1.1 File version= 1.1
> RTFRDR>
> RTFRDR> end if
> RTFRDR> end
> CNSsolve>
> CNSsolve> parameter
> PARRDR> if ( &BLANK%prot_parameter_infile = false ) then
> NEXTCD: condition evaluated as true
> PARRDR> @@&prot_parameter_infile
> ASSFIL: file
> /usr/local/cns/cns_solve_1.1/libraries/toppar/protein_rep.param
> opened.
> PARRDR>remarks file toppar/protein_rep.param
> PARRDR>remarks protein parameters for crystallographic structure
> determination
> PARRDR>remarks with "soft" (purely repulsive) van der Waals parameters.
> PARRDR>remarks
> PARRDR>remarks file toppar/protein_rep.param
> PARRDR>remarks Parameter file including bond and angle parameters
> PARRDR>remarks derived from Cambridge Data Base model structures
> PARRDR>remarks (R. A. Engh and R. Huber, Acta Cryst. Sect. A., 1991).
> PARRDR>remarks
> PARRDR>remarks Nonbonded parameters taken from PROLSQ using REPEL function.
> PARRDR>remarks Small dihedral angle energy constants set to uniform
> small value.
> PARRDR>remarks All other dihedral and improper energy constants set
> to uniform
> PARRDR>remarks large values.
> PARRDR>remarks
> PARRDR>remarks Warning: these parameters are not suitable for free MD
> simulations
> PARRDR>remarks
> PARRDR>
> PARRDR>!
> PARRDR>! References:
> PARRDR>! Engh, R.A. and Huber, R. (1991). Accurate Bond and
> PARRDR>! Angle Parameters for X-ray Protein-Structure Refinement,
> PARRDR>! Acta Cryst. A47, 392-400.
> PARRDR>!
> PARRDR>! Hendrickson W.A. and Konnert J.H. in "Computing in
> PARRDR>! Crystallography" (ed. R. Diamond, S. Ramaseshan
> PARRDR>! and K. Venkatesan) (Bangalore, Indian Institute of
> PARRDR>! Science, 1980) 13.01-13.23
> PARRDR>!
> PARRDR>
> PARRDR>set echo=off message=off end
> Program version= 1.1 File version= 1.1
> PARRDR> end if
> PARRDR> if ( &BLANK%nucl_parameter_infile = false ) then
> NEXTCD: condition evaluated as true
> PARRDR> @@&nucl_parameter_infile
> ASSFIL: file
> /usr/local/cns/cns_solve_1.1/libraries/toppar/dna-rna_rep.param
> opened.
> PARRDR>remarks file toppar/dna-rna_rep.param
> PARRDR>remarks nucleic acid rna-dna parameter file for crystallographic
> PARRDR>remarks structure determination using soft (purely repulsive)
> PARRDR>remarks van der Waals parameters.
> PARRDR>remarks
> PARRDR>remarks Warning: these parameters are not suitable for free MD
> simulations
> PARRDR>remarks
> PARRDR>
> PARRDR>remarks Bases 18.75% Sugar 56.6% Phos 154.8%
> PARRDR>remarks K= scale*(kT/sigma**2), scales=Base 0.1875, Sugar
> 0.566, Phos 1.548
> PARRDR>remarks Nonbonded parameters taken from PROLSQ using REPEL function
> PARRDR>remarks Note: use water parameters in protein_rep.param
> PARRDR>
> PARRDR>! removed references to CA, CF, CS, MG, NH3, OS (ATB 12/30/94)
> PARRDR>! removed TIP3 water model (ATB 12/30/94)
> PARRDR>! mapped NA->NNA, CH3E->CC3E (ATB 12/30/94)
> PARRDR>
> PARRDR>!
> PARRDR>!Please cite the following reference when using these parameters:
> PARRDR>!G. Parkinson, J. Vojtechovsky, L. Clowney, A.T. Brunger, H.M. Berman,
> PARRDR>! New Parameters for the Refinement of Nucleic Acid
> Containing Structures,
> PARRDR>! Acta Cryst. D, 52, 57-64 (1996).
> PARRDR>!
> PARRDR>! Oct. 8, 1996 - Modified by Alexey Bochkarev (McMaster University)
> PARRDR>! to process properly 5PHO (5'-terminus with
> phosphate) patch.
> PARRDR>! Geometry and charges of -O5'-PO3 group were
> taken from
> PARRDR>! Saenger W. 1984. Principles of Nucleic Acid
> Structure
> PARRDR>! All modifications are placed between:
> PARRDR>!***AB***
> PARRDR>!....included fragment
> PARRDR>!***AB end***
> PARRDR>! New atomic types were introduced (see
> dna-rna.top) to describe
> PARRDR>! -O5'-PO3 group: O5H (O5') O1PH (O1P) O2PH (O2P)
> PARRDR>! in addition to existing OH (O5T)
> PARRDR>
> PARRDR>set echo=off message=off end
> Program version= 1.1 File version= 1.1
> PARRDR> end if
> PARRDR> if ( &BLANK%water_parameter_infile = false ) then
> NEXTCD: condition evaluated as true
> PARRDR> @@&water_parameter_infile
> ASSFIL: file
> /usr/local/cns/cns_solve_1.1/libraries/toppar/water_rep.param opened.
> PARRDR>remarks file toppar/water.param
> PARRDR>remarks water parameters for structure determination
> PARRDR>remarks
> PARRDR>
> PARRDR>set echo=false end
> Program version= 1.1 File version= 1.1
> EVALUATE: symbol $VDW_RADIUS_O set to 2.90000 (real)
> EVALUATE: symbol $VDW_RADIUS_HH set to 1.60000 (real)
> EVALUATE: symbol $VDW_RADIUS_O set to 2.58361 (real)
> EVALUATE: symbol $VDW_RADIUS_HH set to 1.42544 (real)
> EVALUATE: symbol $VDW_RADIUS14_O set to 2.31634 (real)
> EVALUATE: symbol $VDW_RADIUS14_HH set to 1.15817 (real)
> EVALUATE: symbol $VDW_EPS set to 0.100000 (real)
> PARRDR>
> PARRDR> end if
> PARRDR> if ( &BLANK%carbo_parameter_infile = false ) then
> NEXTCD: condition evaluated as true
> PARRDR> @@&carbo_parameter_infile
> ASSFIL: file
> /usr/local/cns/cns_solve_1.1/libraries/toppar/carbohydrate.param
> opened.
> PARRDR>remarks file toppar/carbohydrate.param
> PARRDR>REMARKS Parameter file for pyranose sugars for crystallographic
> PARRDR>remarks structure determination.
> PARRDR>remarks
> PARRDR>
> PARRDR>REMARKS Bill Weis 10-July-1988
> PARRDR>REMARKS Additions for atom type combinations not covered in
> PARAM19X.PRO.
> PARRDR>REMARKS Needed additions are for ether oxygen and aliphatic
> carbon in all-atom
> PARRDR>REMARKS representation used for sugars (type CC). Ditto for type HA.
> PARRDR>REMARKS Values from J. Brady glucose parameters unless noted.
> PARRDR>REMARKS These should be sufficient for refinement.
> PARRDR>
> PARRDR>REMARKS Additions 6-March-1992 Bill Weis
> PARRDR>REMARKS New atom types CCA, CCE, OA for the C1 & O1 positions
> to account
> PARRDR>REMARKS for different bond and angle values due to the
> anomeric effect.
> PARRDR>REMARKS More accurate equilibrium values for bond angle around
> this oxygen
> PARRDR>REMARKS in glycosidic linkages. CCE for equatorial O1, CCA for
> PARRDR>REMAKRS axial O1. For free sugar, keep OH1 as O1 atomtype;
> changed to OA
> PARRDR>REMARKS for linkages.
> PARRDR>REMARKS References: G.A. Jeffrey (1990) Acta Cryst B46, 89-103;
> PARRDR>REMARKS K. Hirotsu & A.Shimada, (1974) Bull. Chem. Soc. Japan,
> 47, 1872-1879.
> PARRDR>
> PARRDR>REMARKS This set has been modified to be roughly consistent with
> PARRDR>REMARKS the csd-derived protein parameters of Engh and Huber.
> PARRDR>REMARKS New atom type CC6 for exocyclic 6 carbon
> PARRDR>REMARKS Bill Weis 5/11/92
> PARRDR>
> PARRDR>set echo=false end
> Program version= 1.1 File version= 1.1
> PARRDR>
> PARRDR> end if
> PARRDR> if ( &BLANK%prost_parameter_infile = false ) then
> NEXTCD: condition evaluated as false
> PARRDR> @@&prost_parameter_infile
> PARRDR> end if
> PARRDR> if ( &BLANK%ligand_parameter_infile = false ) then
> NEXTCD: condition evaluated as false
> PARRDR> @@&ligand_parameter_infile
> PARRDR> end if
> PARRDR> if ( &BLANK%ion_parameter_infile = false ) then
> NEXTCD: condition evaluated as true
> PARRDR> @@&ion_parameter_infile
> ASSFIL: file /usr/local/cns/cns_solve_1.1/libraries/toppar/ion.param opened.
> PARRDR>remarks file toppar/ion.param
> PARRDR>remarks nonbonded parameters for common ions
> PARRDR>remarks new parameters derived from literature for single atom species
> PARRDR>remarks PDA 02/09/99
> PARRDR>
> PARRDR>set echo=off end
> Program version= 1.1 File version= 1.1
> PARRDR> end if
> PARRDR> end
> CNSsolve>
> CNSsolve> segment
> SEGMENT> chain
> CHAIN> if ( &convert = true ) then
> NEXTCD: condition evaluated as true
> CHAIN> convert=true
> CHAIN> end if
> CHAIN> if ( &separate = true ) then
> NEXTCD: condition evaluated as true
> CHAIN> separate=true
> CHAIN> end if
> CHAIN> @@&prot_link_infile
> ASSFIL: file
> /usr/local/cns/cns_solve_1.1/libraries/toppar/protein.link opened.
> CHAIN>remarks file toppar/protein.link
> CHAIN>remarks
> CHAIN>remarks this is a macro to define standard protein peptide bonds
> CHAIN>remarks and termini to generate a protein sequence.
> CHAIN>
> CHAIN>set echo=false end
> Program version= 1.1 File version= 1.1
> CHAIN> @@&nucl_link_infile
> ASSFIL: file
> /usr/local/cns/cns_solve_1.1/libraries/toppar/dna-rna.link opened.
> CHAIN>remarks file toppar/dna-rna.link
> CHAIN>remarks macro to define standard nucleic acid links and termini
> CHAIN>remarks this file has both 3' and 5' terminii without phosphate groups
> CHAIN>remarks
> CHAIN>
> CHAIN>set echo=false end
> Program version= 1.1 File version= 1.1
> CHAIN> coordinates @@&coordinate_infile
> SEGMNT: sequence read from coordinate file
> ASSFIL: file Amore.pdb opened.
> COOR>REMARK - BOX = 4.000
> COOR>CRYST1 133.632 133.632 320.765 90.00 90.00 120.00 r 3
> COOR>SCALE1 0.007483 0.004320 -0.000000 -0.00000
> COOR>SCALE2 -0.000000 0.008641 -0.000000 0.00000
> COOR>SCALE3 0.000000 -0.000000 0.003118 -0.00000
> COOR>ATOM 1 N LEU A 9 24.529 39.701 32.467 1.00
> 22.77 N
> MAPIC: Atom numbers being modified
> MAPIC: Atom numbers being modified
> SEGMNT: 379 residues were inserted into segment "A "
> MAPIC: Atom numbers being modified
> MAPIC: Atom numbers being modified
> SEGMNT: 379 residues were inserted into segment "B "
> MAPIC: Atom numbers being modified
> MAPIC: Atom numbers being modified
> SEGMNT: 379 residues were inserted into segment "C "
> MAPIC: Atom numbers being modified
> MAPIC: Atom numbers being modified
> SEGMNT: 379 residues were inserted into segment "D "
> MAPIC: Atom numbers being modified
> MAPIC: Atom numbers being modified
> SEGMNT: 379 residues were inserted into segment "E "
> MAPIC: Atom numbers being modified
> MAPIC: Atom numbers being modified
> SEGMNT: 379 residues were inserted into segment "F "
> MAPIC: Atom numbers being modified
> MAPIC: Atom numbers being modified
> SEGMNT: 379 residues were inserted into segment "G "
> MAPIC: Atom numbers being modified
> MAPIC: Atom numbers being modified
> SEGMNT: 379 residues were inserted into segment "H "
> MAPIC: Atom numbers being modified
> MAPIC: Atom numbers being modified
> SEGMNT: 379 residues were inserted into segment "I "
> MAPIC: Atom numbers being modified
> MAPIC: Atom numbers being modified
> SEGMNT: 379 residues were inserted into segment "J "
> MAPIC: Atom numbers being modified
> MAPIC: Atom numbers being modified
> SEGMNT: 379 residues were inserted into segment "K "
> MAPIC: Atom numbers being modified
> %GENRES error encountered: exceeded MAXB parameter --> recompile program
> (CNS is in mode: SET ABORT=NORMal END)
> *****************************************************
> ABORT mode will terminate program execution.
> *****************************************************
> Program will stop immediately.
> ============================================================
> Maximum dynamic memory allocation: 1544832 bytes
> Maximum dynamic memory overhead: 80 bytes
> Program started at: 15:08:11 on 23-Aug-2007
> Program stopped at: 15:08:52 on 23-Aug-2007
> CPU time used: 39.4800 seconds
> ============================================================
>
>
>
>
> ************************************************
> Dr. N.SAMPATH
> Post Doctoral Fellow
> Department of Molecular & Cell Biology
> Samsung Biomedical Research Institute
> Sungkyunkwan Univ. School of Medicine
> Suwon 440-746, S.Korea
> ************************************************
> tel : 82-31-299-6150 & 82-31-299-6155
> ************************************************
>
>
>
>
> ---------------------------------
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_____________________________________________
- Joshua Warren, PhD ([log in to unmask]) -
- 212 Nanaline H. Duke -
- DUMC -
- home: (919) 918 7860 -
- work: (919) 681 5266 -
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