NMR Restraints Grid
| |
NMR Restraints Grid |
|
Result table
| image | mrblock_id | pdb_id | bmrb_id | cing | stage | position | program | type |
|
|
538135 |
2lj9   |
17926 | cing | 1-original | 5 | XPLOR/CNS | unknown |
{+ file: anneal.inp +}
{+ directory: nmr_calc +}
{+ description: dynamical annealing with NOEs, coupling constants,
chemical shift restraints starting from extended
strands or pre-folded structures. +}
{+ authors: Gregory Warren, Michael Nilges, John Kuszewski,
Marius Clore and Axel Brunger +}
{+ copyright: Yale University +}
{+ reference: Clore GM, Gronenborn AM, Tjandra N, Direct structure refinement
against residual dipolar couplings in the presence of rhombicity
of unknown magnitude., J. Magn. Reson., 131, In press, (1998) +}
{+ reference: Clore GM, Gronenborn AM, Bax A, A robust method for determining
the magnitude of the fully asymmetric alignment tensor of
oriented macromolecules in the absence of structural
information., J. Magn. Reson., In press (1998) +}
{+ reference: Garrett DS, Kuszewski J, Hancock TJ, Lodi PJ, Vuister GW,
Gronenborn AM, Clore GM, The impact of direct refinement against
three-bond HN-C alpha H coupling constants on protein structure
determination by NMR., J. Magn. Reson. Ser. B, 104(1),
99-103, (1994) May +}
{+ reference: Kuszewski J, Qin J, Gronenborn AM, Clore GM, The impact of direct
refinement against 13C alpha and 13C beta chemical shifts on
protein structure determination by NMR., J. Magn. Reson. Ser. B,
106(1), 92-6, (1995) Jan +}
{+ reference: Kuszewski J, Gronenborn AM, Clore GM, The impact of direct
refinement against proton chemical shifts on protein structure
determination by NMR., J. Magn. Reson. Ser. B, 107(3), 293-7,
(1995) Jun +}
{+ reference: Kuszewski J, Gronenborn AM, Clore GM, A potential involving
multiple proton chemical-shift restraints for
nonstereospecifically assigned methyl and methylene protons.
J. Magn. Reson. Ser. B, 112(1), 79-81, (1996) Jul. +}
{+ reference: Nilges M, Gronenborn AM, Brunger AT, Clore GM, Determination
of three-dimensional structures of proteins by simulated
annealing with interproton distance restraints: application
to crambin, potato carboxypeptidase inhibitor and barley
serine proteinase inhibitor 2. Protein Engineering 2,
27-38, (1988) +}
{+ reference: Nilges M, Clore GM, Gronenborn AM, Determination of
three-dimensional structures of proteins from interproton
distance data by dynamical simulated annealing from a random
array of atoms. FEBS LEtt. 239, 129-136. (1988) +}
{+ reference: Rice LM, Brunger AT, Torsion Angle Dynamics: Reduced Variable
Conformational Sampling Enhances Crystallographic Structure
Refinement., Proteins, 19, 277-290 (1994) +}
{+ reference: Stein EG, Rice LM, Brunger AT, Torsion angle molecular
dynamics: a new efficient tool for NMR structure calculation.,
J. Mag. Res. Ser. B 124, 154-164 (1997) +}
{+ reference: Tjandra N, Garrett DS, Gronenborn AM, Bax A, Clore GM, Defining
long range order in NMR structure determination from the
dependence of heteronuclear relaxation times on rotational
diffusion anisotropy. Nature Struct. Biol., 4(6), 443-9,
(1997) June +}
{+ reference: Tjandra N, Omichinski JG, Gronenborn AM, Clore GM, Bax A, Use of
dipolar 1H-15N and 1H-13C couplings in the structure
determination of magnetically oriented macromolecules in
solution. Nature Struct. Biol., 4(9), 732-8, (1997) Sept +}
! Data taken from: Qin J, Clore GM, Kennedy WP, Kuszewski J, Gronenborn AM,
! The solution structure of human thioredoxin complexed with
! its target from Ref-1 reveals peptide chain reversal.,
! Structure, 4(5), 613-620, 1996 May 15.
{- Guidelines for using this file:
- all strings must be quoted by double-quotes
- logical variables (true/false) are not quoted
- do not remove any evaluate statements from the file -}
{- begin block parameter definition -} define(
{======================= molecular structure =========================}
{* parameter file(s) *}
{===>} par.1="CNS_TOPPAR:protein-allhdg.param";
{===>} par.2="";
{===>} par.3="";
{===>} par.4="";
{===>} par.5="";
{* structure file(s) *}
{===>} struct.1="generate_seq.mtf";
{===>} struct.2="";
{===>} struct.3="";
{===>} struct.4="";
{===>} struct.5="";
{* input coordinate file(s) *}
{===>} pdb.in.file.1="shortcp12_extended.pdb";
{===>} pdb.in.file.2="";
{===>} pdb.in.file.3="";
{========================== atom selection ===========================}
{* input "backbone" selection criteria for average structure generation *}
{* for protein (name n or name ca or name c)
for nucleic acid (name O5' or name C5' or name C4' or name C3'
or name O3' or name P) *}
{===>} pdb.atom.select=(name n or name ca or name c);
{====================== refinement parameters ========================}
{* type of molecular dynamics for hot phase *}
{+ choice: "torsion" "cartesian" +}
{===>} md.type.hot="torsion";
{* type of molecular dynamics for cool phase *}
{+ choice: "torsion" "cartesian" +}
{===>} md.type.cool="torsion";
{* refine using different initial velocities or coordinates
(enter base name in "input coordinate files" field) *}
{+ choice: "veloc" "coord" +}
{===>} md.type.initial="veloc";
{* seed for random number generator *}
{* change to get different initial velocities *}
{===>} md.seed=82364;
{* select whether the number of structures will be either trial or
accepted structures and whether to print only the trial, accepted,
both sets of structures. *}
{+ list: The printing format is as follows:
trial = pdb.out.name + _#.pdb , accepted = pdb.out.name + a_#.pdb +}
{* are the number of structures to be trials or accepted? *}
{+ choice: "trial" "accept" +}
{===>} flg.trial.struc="trial";
{* number of trial or accepted structures *}
{===>} pdb.end.count=150;
{* print accepted structures *}
{+ choice: true false +}
{===>} flg.print.accept=false;
{* print trial structures *}
{+ choice: true false +}
{===>} flg.print.trial=true;
{* calculate an average structure for either the trial or
accepted structure. If calculate accepted average is false then
an average for the trial structures will be calculated. *}
{* calculate an average structure? *}
{+ choice: true false +}
{===>} flg.calc.ave.struct=false;
{* calculate an average structure for the accepted structures? *}
{+ choice: true false +}
{===>} flg.calc.ave.accpt=false;
{* minimize average coordinates? *}
{+ choice: true false +}
{===>} flg.min.ave.coor=false;
{=================== torsion dynamics parameters ====================}
{* maximum unbranched chain length (use <= 0 for automatic) *}
{===>} md.torsion.maxlength=0;
{* maximum number of distinct bodies (use <= 0 for automatic) *}
{===>} md.torsion.maxtree=0;
{========== parameters for high temperature annealing stage ==========}
{* temperature (proteins: 50000, dna/rna: 20000) *}
{===>} md.hot.temp=50000;
{* number of steps (proteins: 1000, dna/rna: 4000) *}
{===>} md.hot.step=1000;
{* scale factor to reduce van der Waals (repel) energy term *}
{===>} md.hot.vdw=0.1;
{* scale factor for NOE energy term *}
{===>} md.hot.noe=150;
{* scale factor for dihedral angle energy term (proteins: 100, dna/rna: 5) *}
{===>} md.hot.cdih=100;
{* molecular dynamics timestep *}
{===>} md.hot.ss=0.015;
{======== parameters for the first slow-cool annealing stage =========}
{* temperature (cartesian: 1000, torsion: [proteins: 50000, dna/rna: 20000]) *}
{===>} md.cool.temp=50000;
{* number of steps *}
{===>} md.cool.step=1000;
{* scale factor for final van der Waals (repel) energy term
(cartesian: 4.0, torsion: 1.0) *}
{===>} md.cool.vdw=1.0;
{* scale factor for NOE energy term *}
{===>} md.cool.noe=150;
{* scale factor for dihedral angle energy term *}
{===>} md.cool.cdih=200;
{* molecular dynamics timestep (cartesian: 0.005, torsion: 0.015) *}
{===>} md.cool.ss=0.015;
{* slow-cool annealing temperature step (cartesian: 25, torsion: 250) *}
{===>} md.cool.tmpstp=250;
{========= parameters for a second slow-cool annealing stage ==========}
{* cartesian slow-cooling annealing stage to be used only with torsion
slow-cool annealing stage *}
{* this stage is only necessary when the macromolecule is a protein
greater than 160 residues or in some cases for nucleic acids *}
{* use cartesian cooling stage? *}
{+ choice: true false +}
{===>} md.cart.flag=true;
{* temperature *}
{===>} md.cart.temp=2000;
{* number of steps *}
{===>} md.cart.step=3000;
{* scale factor for initial van der Waals (repel) energy term *}
{===>} md.cart.vdw.init=1.0;
{* scale factor for final van der Waals (repel) energy term *}
{===>} md.cart.vdw.finl=4.0;
{* scale factor for NOE energy term *}
{===>} md.cart.noe=150;
{* scale factor for dihedral angle energy term *}
{===>} md.cart.cdih=200;
{* molecular dynamics timestep *}
{===>} md.cart.ss=0.005;
{* slow-cool annealing temperature step *}
{===>} md.cart.tmpstp=25;
{=============== parameters for final minimization stage ==============}
{* scale factor for NOE energy term *}
{===>} md.pow.noe=75;
{* scale factor for dihedral angle energy term *}
{===>} md.pow.cdih=400;
{* number of minimization steps *}
{===>} md.pow.step=200;
{* number of cycles of minimization *}
{===>} md.pow.cycl=10;
{============================= noe data ===============================}
{- Important - if you do not have a particular data set then
set the file name to null ("") -}
{* NOE distance restraints files. *}
{* restraint set 1 file *}
{===>} nmr.noe.file.1="cp12_noe_all20100820_5758.tbl";
{* restraint set 2 file *}
{===>} nmr.noe.file.2="cp12_noe_all20100820_6978.tbl";
{* restraint set 3 file *}
{===>} nmr.noe.file.3="cp12_noe_all20100820_6068.tbl";
{* restraint set 4 file *}
{===>} nmr.noe.file.4="hbond.tbl";
{* restraint set 5 file *}
{===>} nmr.noe.file.5="";
{* NOE averaging modes *}
{* restraint set 1 *}
{+ choice: "sum" "cent" "R-6" "R-3" "symm" +}
{===>} nmr.noe.ave.mode.1="sum";
{* restraint set 2 *}
{+ choice: "sum" "cent" "R-6" "R-3" "symm" +}
{===>} nmr.noe.ave.mode.2="sum";
{* restraint set 3 *}
{+ choice: "sum" "cent" "R-6" "R-3" "symm" +}
{===>} nmr.noe.ave.mode.3="sum";
{* restraint set 4 *}
{+ choice: "sum" "cent" "R-6" "R-3" "symm" +}
{===>} nmr.noe.ave.mode.4="sum";
{* restraint set 5 *}
{+ choice: "sum" "cent" "R-6" "R-3" "symm" +}
{===>} nmr.noe.ave.mode.5="sum";
{======================== hydrogen bond data ==========================}
{* hydrogen-bond distance restraints file. *}
{===>} nmr.noe.hbnd.file="";
{* enter hydrogen-bond distance averaging mode *}
{+ choice: "sum" "cent" "R-6" "R-3" "symm" +}
{===>} nmr.noe.ave.mode.hbnd="sum";
{======================= 3-bond J-coupling data =======================}
{* the default setup is for the phi dihedral *}
{* Class 1 *}
{* 3-bond J-coupling non-glycine restraints file *}
{===>} nmr.jcoup.file.1="";
{* 3-bond J-coupling non-glycine potential *}
{+ choice: "harmonic" "square" "multiple" +}
{===>} nmr.jcoup.pot.1="harmonic";
{* 3-bond J-coupling non-glycine force value *}
{===>} nmr.jcoup.force.1.1=1;
{* 3-bond j-coupling multiple class force second value *}
{===>} nmr.jcoup.force.2.1=0;
{* 3-bond j-coupling Karplus coefficients *}
{* the default values are for phi *}
{===>} nmr.jcoup.coef.1.1=6.98;
{===>} nmr.jcoup.coef.2.1=-1.38;
{===>} nmr.jcoup.coef.3.1=1.72;
{===>} nmr.jcoup.coef.4.1=-60.0;
{* Class 2 *}
{* 3-bond j-coupling glycine restraints files *}
{===>} nmr.jcoup.file.2="";
{* 3-bond J-coupling glycine potential *}
{* The potential for the glycine class must be multiple *}
{+ choice: "harmonic" "square" "multiple" +}
{===>} nmr.jcoup.pot.2="multiple";
{* 3-bond J-coupling first force value *}
{===>} nmr.jcoup.force.1.2=1;
{* 3-bond j-coupling glycine or multiple force second value *}
{===>} nmr.jcoup.force.2.2=0;
{* 3-bond j-coupling Karplus coefficients *}
{* the default values are for glycine phi *}
{===>} nmr.jcoup.coef.1.2=6.98;
{===>} nmr.jcoup.coef.2.2=-1.38;
{===>} nmr.jcoup.coef.3.2=1.72;
{===>} nmr.jcoup.coef.4.2=0.0;
{================ 1-bond heteronuclear J-coupling data ================}
{* Class 1 *}
{* 1-bond heteronuclear j-coupling file *}
{===>} nmr.oneb.file.1="";
{* 1-bond heteronuclear j-coupling potential *}
{+ choice: "harmonic" "square" +}
{===>} nmr.oneb.pot.1="harmonic";
{* 1-bond heteronuclear j-coupling force value *}
{===>} nmr.oneb.force.1=1.0;
{=============== alpha/beta carbon chemical shift data ================}
{* Class 1 *}
{* carbon, alpha and beta, chemical shift restraints file *}
{===>} nmr.carb.file.1="";
{* carbon, alpha and beta, chemical shift restraint potential *}
{+ choice: "harmonic" "square" +}
{===>} nmr.carb.pot.1="harmonic";
{* carbon, alpha and beta, chemical shift restraint force value *}
{===>} nmr.carb.force.1=0.5;
{===================== proton chemical shift data =====================}
{* Class 1 *}
{* class 1 proton chemical shift restraints file *}
{===>} nmr.prot.file.1="";
{* class 1 proton chemical shift potential *}
{+ choice: "harmonic" "square" "multiple" +}
{===>} nmr.prot.pot.1="harmonic";
{* class 1 proton chemical shift force value *}
{===>} nmr.prot.force.1.1=7.5;
{* 2nd class 1 proton chemical shift force value for multi *}
{===>} nmr.prot.force.2.1=0;
{* class 1 proton chemical shift violation cutoff threshold *}
{===>} nmr.prot.thresh.1=0.3;
{* Class 2 *}
{* class 2 proton chemical shift restraints file *}
{===>} nmr.prot.file.2="";
{* class 2 proton chemical shift potential *}
{+ choice: "harmonic" "square" "multiple" +}
{===>} nmr.prot.pot.2="harmonic";
{* class 2 proton chemical shift force value *}
{===>} nmr.prot.force.1.2=7.5;
{* 2nd class 2 proton chemical shift force value for multi *}
{===>} nmr.prot.force.2.2=0;
{* class 2 proton chemical shift violation cutoff threshold *}
{===>} nmr.prot.thresh.2=0.3;
{* Class 3 *}
{* class 3 proton chemical shift restraints file *}
{===>} nmr.prot.file.3="";
{* class 3 proton chemical shift potential *}
{+ choice: "harmonic" "square" "multiple" +}
{===>} nmr.prot.pot.3="harmonic";
{* class 3 proton chemical shift force value *}
{===>} nmr.prot.force.1.3=7.5;
{* 2nd class 3 proton chemical shift force value for multi *}
{===>} nmr.prot.force.2.3=0;
{* class 3 proton chemical shift violation cutoff threshold *}
{===>} nmr.prot.thresh.3=0.3;
{* Class 4 *}
{* class 4 proton chemical shift restraints file *}
{===>} nmr.prot.file.4="";
{* class 4 proton chemical shift potential *}
{+ choice: "harmonic" "square" "multiple" +}
{===>} nmr.prot.pot.4="multiple";
{* class 4 proton chemical shift force value *}
{===>} nmr.prot.force.1.4=7.5;
{* 2nd class 4 proton chemical shift force value for multi *}
{===>} nmr.prot.force.2.4=0;
{* class 4 proton chemical shift violation cutoff threshold *}
{===>} nmr.prot.thresh.4=0.3;
{================ diffusion anisotropy restraint data =================}
{* fixed or harmonically restrained external axis *}
{+ choice: "fixed" "harm" +}
{===>} nmr.dani.axis="harm";
{* Class 1 *}
{* diffusion anisotropy restraints file *}
{===>} nmr.dani.file.1="";
{* diffusion anisotropy potential *}
{+ choice: "harmonic" "square" +}
{===>} nmr.dani.pot.1="harmonic";
{* diffusion anisotropy initial force value *}
{===>} nmr.dani.force.init.1=0.01;
{* diffusion anisotropy final force value *}
{===>} nmr.dani.force.finl.1=1.0;
{* diffusion anisotropy coefficients *}
{* coef: *}
{* Tc = 1/2(Dx+Dy+Dz) in *}
{===>} nmr.dani.coef.1.1=13.1;
{* anis = Dz/0.5*(Dx+Dy) *}
{===>} nmr.dani.coef.2.1=2.1;
{* rhombicity = 1.5*(Dy-Dx)/(Dz-0.5*(Dy+Dx)) *}
{===>} nmr.dani.coef.3.1=0.0;
{* wH in *}
{===>} nmr.dani.coef.4.1=600.13;
{* wN in *}
{===>} nmr.dani.coef.5.1=60.82;
{============= susceptability anisotropy restraint data ===============}
{* fixed or harmonically restrained external axis *}
{+ choice: "fixed" "harm" +}
{===>} nmr.sani.axis="harm";
{* Class 1 *}
{* susceptability anisotropy restraints file *}
{===>} nmr.sani.file.1="";
{* susceptability anisotropy potential *}
{+ choice: "harmonic" "square" +}
{===>} nmr.sani.pot.1="harmonic";
{* susceptability anisotropy initial force value *}
{===>} nmr.sani.force.init.1=0.01;
{* susceptability anisotropy final force value *}
{===>} nmr.sani.force.finl.1=50.0;
{* susceptability anisotropy coefficients *}
{* coef: ;
a0+a1*(3*cos(theta)^2-1)+a2*(3/2)*sin(theta)^2*cos(2*phi) *}
{* DFS = a0 *}
{===>} nmr.sani.coef.1.1=-0.0601;
{* axial = a0-a1-3/2*a2 *}
{===>} nmr.sani.coef.2.1=-8.02;
{* rhombicity = a2/a1 *}
{===>} nmr.sani.coef.3.1=0.4;
{======================== other restraint data ========================}
{* dihedral angle restraints file *}
{* Note: the restraint file MUST NOT contain restraints
dihedral or end *}
{===>} nmr.cdih.file="CNS_talos30.tbl";
{* DNA-RNA base planarity restraints file *}
{* Note: include weights as $pscale in the restraint file *}
{===>} nmr.plan.file="";
{* input planarity scale factor - this will be written into $pscale *}
{===>} nmr.plan.scale=150;
{* NCS-restraints file *}
{* example is in inputs/xtal_data/eg1_ncs_restrain.dat *}
{===>} nmr.ncs.file="";
{======================== input/output files ==========================}
{* base name for input coordinate files *}
{===>} pdb.in.name="";
{* base name for output coordinate files *}
{===>} pdb.out.name="shortcp12_noe5778_talos30";
{===========================================================================}
{ things below this line do not normally need to be changed }
{ except for the torsion angle topology setup if you have }
{ molecules other than protein or nucleic acid }
{===========================================================================}
flg.cv.flag=false;
flg.cv.noe=false;
flg.cv.coup=false;
flg.cv.cdih=false;
flg.dgsa.flag=false;
nmr.cv.numpart=10;
) {- end block parameter definition -}
checkversion 1.2
evaluate ($log_level=quiet)
structure
if (&struct.1 # "") then
@@&struct.1
end if
if (&struct.2 # "") then
@@&struct.2
end if
if (&struct.3 # "") then
@@&struct.3
end if
if (&struct.4 # "") then
@@&struct.4
end if
if (&struct.5 # "") then
@@&struct.5
end if
end
if ( &BLANK%pdb.in.file.1 = false ) then
coor @@&pdb.in.file.1
end if
if ( &BLANK%pdb.in.file.2 = false ) then
coor @@&pdb.in.file.2
end if
if ( &BLANK%pdb.in.file.3 = false ) then
coor @@&pdb.in.file.3
end if
parameter
if (&par.1 # "") then
@@&par.1
end if
if (&par.2 # "") then
@@&par.2
end if
if (&par.3 # "") then
@@&par.3
end if
if (&par.4 # "") then
@@&par.4
end if
if (&par.5 # "") then
@@&par.5
end if
end
if ( $log_level = verbose ) then
set message=normal echo=on end
else
set message=off echo=off end
end if
parameter
nbonds
repel=0.80
rexp=2 irexp=2 rcon=1.
nbxmod=3
wmin=0.01
cutnb=6.0 ctonnb=2.99 ctofnb=3.
tolerance=1.5
end
end
{- Read experimental data -}
@CNS_NMRMODULE:readdata ( nmr=&nmr;
flag=&flg;
output=$nmr; )
{- Read and store the number of NMR restraints -}
@CNS_NMRMODULE:restraintnumber ( num=$num; )
{- Set mass values -}
do (fbeta=10) (all)
do (mass=100) (all)
evaluate ($nmr.trial.count = 0) {- Initialize current structure number -}
evaluate ($nmr.accept.count = 0) {- Initialize number accepted -}
evaluate ($nmr.counter = 0)
evaluate ($nmr.prev.counter = -1)
@CNS_NMRMODULE:initave ( ave=$ave;
ave2=$ave2;
cv=$cv;
ener1=$ener1;
ener2=$ener2;
flag=&flg;
nmr.prot=&nmr.prot; )
{- Zero the force constant of disulfide bonds. -}
parameter
bonds ( name SG ) ( name SG ) 0. TOKEN
end
{- define a distance restraints for each disulfide bond, i.e.,
treat it as if it were an NOE. -}
for $ss_rm_id_1 in id ( name SG ) loop STRM
for $ss_rm_id_2 in id ( name SG and
bondedto ( id $ss_rm_id_1 ) ) loop STR2
if ($ss_rm_id_1 > $ss_rm_id_2) then
pick bond ( id $ss_rm_id_1 ) ( id $ss_rm_id_2 ) equil
evaluate ($ss_bond=$result)
noe
assign ( id $ss_rm_id_1 ) ( id $ss_rm_id_2 ) $ss_bond 0.1 0.1
end
end if
end loop STR2
end loop STRM
{- Count the number of residues and determine molecule type -}
identify (store9) (tag)
evaluate ($nmr.rsn.num = $SELECT)
identify (store9) ( tag and ( resn THY or resn CYT or resn GUA or
resn ADE or resn URI ))
evaluate ($nmr.nucl.num = $SELECT)
{- Improve geometry for torsion angle molecular dynamics -}
evaluate ($flag_tad=false)
if ( &md.type.hot = "torsion" ) then
if ($nmr.nucl.num > 0) then
flag exclude * include bond angl impr dihed vdw end
minimize powell nstep=2000 drop=10. nprint=100 end
else
flag exclude * include bond angl impr vdw end
minimize powell nstep=2000 drop=10. nprint=100 end
end if
evaluate ($flag_tad=true)
end if
if ( &md.type.cool="torsion") then
evaluate ($flag_tad=true)
end if
if (&nmr.dani.axis = "harm") then
do (harmonic=20.0) (resid 500 and name OO)
do (harmonic=0.0) (resid 500 and name Z )
do (harmonic=0.0) (resid 500 and name X )
do (harmonic=0.0) (resid 500 and name Y )
do (harmonic=0.0) (not (resid 500))
restraints harmonic exponent=2 end
elseif (&nmr.sani.axis = "harm") then
do (harmonic=20.0) (resid 500 and name OO)
do (harmonic=0.0) (resid 500 and name Z )
do (harmonic=0.0) (resid 500 and name X )
do (harmonic=0.0) (resid 500 and name Y )
do (harmonic=0.0) (not (resid 500))
restraints harmonic exponent=2 end
end if
do (refx=x) ( all )
do (refy=y) ( all )
do (refz=z) ( all )
set seed=&md.seed end
{- Begin protocol to generate structures -- loop until done -}
while (&pdb.end.count > $nmr.counter) loop main
{- Set parameter values -}
parameter
nbonds
repel=0.80
rexp=2 irexp=2 rcon=1.
nbxmod=3
wmin=0.01
cutnb=6.0 ctonnb=2.99 ctofnb=3.
tolerance=1.5
end
end
evaluate ($nmr.trial.count = $nmr.trial.count + 1)
if (&md.type.initial = "coord") then
if ($nmr.trial.count < &pdb.end.count) then
evaluate ($coor_count = $nmr.trial.count)
evaluate ($coor_count_init=0.)
else
evaluate ($coor_count_init=$coor_count_init+1)
evaluate ($coor_count = $coor_count_init)
if ($coor_count_init > &pdb.end.count ) then
evaluate ($coor_count = 1)
end if
end if
set remarks=reset end
evaluate ($in_file = &pdb.in.name + "_" + encode($coor_count) + ".pdb")
coor @@$in_file
else
do (x=refx) ( all )
do (y=refy) ( all )
do (z=refz) ( all )
end if
if (&nmr.dani.axis = "fixed" ) then
fix
select=(resname ANI)
end
elseif (&nmr.sani.axis = "fixed" ) then
fix
select=(resname ANI)
end
end if
do ( vx = maxwell(0.5) ) ( all )
do ( vy = maxwell(0.5) ) ( all )
do ( vz = maxwell(0.5) ) ( all )
flags exclude *
include bond angle dihe impr vdw
noe cdih coup oneb carb ncs dani
sani harm end
{- scaling of nmr restraint data during hot dynamics -}
@CNS_NMRMODULE:scalehot ( md=&md;
nmr=&nmr;
input.noe.scale=&md.hot.noe;
input.cdih.scale=&md.hot.cdih; )
{- Zero the force constant of disulfide bonds. -}
parameter
bonds ( name SG ) ( name SG ) 0. TOKEN
end
if ($flag_tad=true) then
{- initialize torsion dynamics topology for this iteration -}
dyna torsion
topology
maxlength=&md.torsion.maxlength
maxtree=&md.torsion.maxtree
{- All dihedrals w/ (force constant > 23) will be locked -}
{- This keeps planar groups planar -}
kdihmax = 23.
@CNS_TOPPAR:torsionmdmods
end
end
end if
{- High temperature dynamics -}
if ( &md.type.hot = "torsion" ) then
igroup
interaction (chemical h* ) (all) weights * 1 vdw 0. elec 0. end
interaction (not chemical h* ) (not chemical h*) weights * 1 vdw &md.hot.vdw
end
end
dyna torsion
cmperiodic=500
vscaling = false
tcoupling = true
timestep = &md.hot.ss
nstep = &md.hot.step
nprint = 50
temperature = &md.hot.temp
end
else
evalutate ($md.hot.nstep1=int(&md.hot.step* 2. / 3. ))
evalutate ($md.hot.nstep2=int(&md.hot.step* 1. / 3. ))
noe asymptote * 0.1 end
parameter nbonds repel=1. end end
igroup
interaction (chemical h* ) (all) weights * 1 vdw 0. elec 0. end
interaction (not chemical h* ) (not chemical h*) weights * 1 angl 0.4 impr 0.1
vdw &md.hot.vdw end
end
dynamics cartesian
cmperiodic=500
vscaling = true
tcoupling=false
timestep=&md.hot.ss
nstep=$md.hot.nstep1
nprint=50
temperature=&md.hot.temp
end
noe asymptote * 1.0 end
igroup
interaction (chemical h* ) (all) weights * 1 vdw 0. elec 0. end
interaction (not chemical h* ) (not chemical h*) weights * 1 vdw &md.hot.vdw end
end
dynamics cartesian
cmperiodic=500
vscaling = true
tcoupling=false
timestep=&md.hot.ss
nstep=$md.hot.nstep2
nprint=50
temperature=&md.hot.temp
end
end if
{- The first slow-cooling with torsion angle dynamics -}
flags include plan end
{- Increase the disulfide bond force constants to their full strength -}
parameter
bonds ( name SG ) ( name SG ) 1000. TOKEN
end
evaluate ($final_t = 0)
evaluate ($ncycle = int((&md.cool.temp-$final_t)/&md.cool.tmpstp))
evaluate ($nstep = int(&md.cool.step/$ncycle))
evaluate ($ini_vdw = &md.hot.vdw)
evaluate ($fin_vdw = &md.cool.vdw)
evaluate ($vdw_step = ($fin_vdw-$ini_vdw)/$ncycle)
if (&md.type.cool = "cartesian") then
evaluate ($vdw_step = (&md.cool.vdw/&md.hot.vdw)^(1/$ncycle))
evaluate ($ini_rad = 0.9)
evaluate ($fin_rad = 0.8)
evaluate ($rad_step = ($ini_rad-$fin_rad)/$ncycle)
evaluate ($radius= $ini_rad)
do (vx=maxwell(&md.cool.temp)) ( all )
do (vy=maxwell(&md.cool.temp)) ( all )
do (vz=maxwell(&md.cool.temp)) ( all )
end if
{- set up nmr restraint scaling -}
evaluate ($kdani.inter.flag=false)
evaluate ($ksani.inter.flag=false)
evaluate ($kdani.cart.flag=false)
evaluate ($ksani.cart.flag=false)
if (&md.cart.flag=true) then
evaluate ($kdani.inter.flag=true)
evaluate ($ksani.inter.flag=true)
@CNS_NMRMODULE:scalecoolsetup ( kdani=$kdani;
ksani=$ksani;
nmr=&nmr;
input.noe.scale=&md.cool.noe;
input.cdih.scale=&md.cool.cdih;
input.ncycle=$ncycle; )
evaluate ($kdani.cart.flag=true)
evaluate ($ksani.cart.flag=true)
else
@CNS_NMRMODULE:scalecoolsetup ( kdani=$kdani;
ksani=$ksani;
nmr=&nmr;
input.noe.scale=&md.cool.noe;
input.cdih.scale=&md.cool.cdih;
input.ncycle=$ncycle; )
end if
evaluate ($bath = &md.cool.temp)
evaluate ($k_vdw = $ini_vdw)
evaluate ($i_cool = 0)
while ($i_cool <= $ncycle) loop cool
evaluate ($i_cool = $i_cool + 1)
igroup
interaction (chemical h*) (all) weights * 1 vdw 0. elec 0. end
interaction (not chemical h*) (not chemical h*) weights * 1 vdw $k_vdw end
end
if ( &md.type.cool = "torsion" ) then
dynamics torsion
cmremove=true
vscaling = true
tcoup = false
timestep = &md.cool.ss
nstep = $nstep
nprint = $nstep
temperature = $bath
end
else
dynamics cartesian
cmremove=true
vscaling = true
tcoup = false
timestep = &md.cool.ss
nstep = $nstep
nprint = $nstep
temperature = $bath
end
end if
if (&md.type.cool = "cartesian") then
evaluate ($radius=max($fin_rad,$radius-$rad_step))
parameter nbonds repel=$radius end end
evaluate ($k_vdw=min($fin_vdw,$k_vdw*$vdw_step))
else
evaluate ($k_vdw= $k_vdw + $vdw_step)
end if
evaluate ($bath = $bath - &md.cool.tmpstp)
@CNS_NMRMODULE:scalecool ( kdani=$kdani;
ksani=$ksani;
nmr=&nmr; )
end loop cool
{- A second slow-cooling with cartesian dyanmics -}
evaluate ($flag_cart=false)
if (&md.cart.flag=true) then
if (&md.type.cool = "torsion") then
evaluate ($flag_cart=true)
dynamics torsion
topology
reset
end
end
evaluate ($cart_nucl_flag=false)
if ($nmr.nucl.num > 0) then
evaluate ($cart_nucl_flag=true)
parameter
nbonds
repel=0
nbxmod=5
wmin=0.01
tolerance=0.5
cutnb=11.5 ctonnb=9.5 ctofnb=10.5
rdie vswitch switch
end
end
flags include elec end
end if
evaluate ($ncycle=int((&md.cart.temp-$final_t)/&md.cart.tmpstp))
evaluate ($nstep=int(&md.cart.step/$ncycle))
evaluate ($vdw_step=(&md.cart.vdw.finl/&md.cart.vdw.init)^(1/$ncycle))
evaluate ($ini_rad=0.9)
evaluate ($fin_rad=0.8)
evaluate ($rad_step=($ini_rad-$fin_rad)/$ncycle)
evaluate ($radius=$ini_rad)
@CNS_NMRMODULE:scalecoolsetup ( kdani=$kdani;
ksani=$ksani;
nmr=&nmr;
input.noe.scale=&md.cart.noe;
input.cdih.scale=&md.cart.cdih;
input.ncycle=$ncycle; )
do (vx=maxwell(&md.cart.temp)) ( all )
do (vy=maxwell(&md.cart.temp)) ( all )
do (vz=maxwell(&md.cart.temp)) ( all )
evaluate ($bath=&md.cart.temp)
evaluate ($k_vdw=&md.cart.vdw.init)
evaluate ($i_cool = 0)
while ($i_cool <= $ncycle) loop cart
evaluate ($i_cool = $i_cool + 1)
igroup
interaction (chemical h*) (all) weights * 1 vdw 0. elec 0. end
interaction (not chemical h*) (not chemical h*) weights * 1 vdw $k_vdw
end
end
dynamics cartesian
vscaling = true
tcoup = false
timestep = &md.cart.ss
nstep = $nstep
nprint = $nstep
temperature = $bath
end
if ($cart_nucl_flag=false) then
evaluate ($radius=max($fin_rad,$radius-$rad_step))
parameter nbonds repel=$radius end end
end if
evaluate ($k_vdw=min(&md.cart.vdw.finl,$k_vdw*$vdw_step))
evaluate ($bath=$bath-&md.cart.tmpstp)
@CNS_NMRMODULE:scalecool ( kdani=$kdani;
ksani=$ksani;
nmr=&nmr; )
end loop cart
end if
end if
{- reset torsion angle topology -}
if ( $flag_tad=true ) then
if ($flag_cart=false) then
dynamics torsion
topology
reset
end
end
end if
end if
{- Final minimization -}
{- turn on proton chemical shifts -}
flags include prot end
noe
scale * &md.pow.noe
end
restraints dihedral
scale = &md.pow.cdih
end
igroup interaction ( all ) ( all ) weights * 1 end end
evaluate ($count=0 )
evaluate ($nmr.min.num=0.)
while (&md.pow.cycl > $count) loop pmini
evaluate ($count=$count + 1)
minimize powell nstep=&md.pow.step drop=10.0 nprint=25 end
evaluate ($nmr.min.num=$nmr.min.num + $mini_cycles)
end loop pmini
{- translate the geometric center of the structure to the origin -}
if ($num.dani > 0. ) then
elseif ($num.sani > 0. ) then
else
show ave ( x ) ( all )
evaluate ($geom_x=-$result)
show ave ( y ) ( all )
evaluate ($geom_y=-$result)
show ave ( z ) ( all )
evaluate ($geom_z=-$result)
coor translate vector=( $geom_x $geom_y $geom_z ) selection=( all ) end
end if
@CNS_NMRMODULE:printaccept ( ave=$ave;
ave2=$ave2;
cv=$cv;
ener1=$ener1;
ener2=$ener2;
flag=&flg;
md=&md;
nmr=&nmr;
num=$num;
output=$nmr;
pdb=&pdb; )
end loop main
@CNS_NMRMODULE:calcave ( ave=$ave;
ave2=$ave2;
cv=$cv;
ener1=$ener1;
ener2=$ener2;
flag=&flg;
md=&md;
nmr=&nmr;
num=$num;
output=$nmr;
pdb=&pdb; )
stop
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