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
************************************************
---------------------------------
Be a better Heartthrob. Get better relationship answers from someone
who knows.
Yahoo! Answers - Check it out.
