NMR Restraints Grid
| |
NMR Restraints Grid |
|
Result table
| image | mrblock_id | pdb_id | bmrb_id | cing | stage | position | program | type |
|
|
538131 |
2lj9   |
17926 | cing | 1-original | 1 | XPLOR/CNS | unknown |
{+ file: accept.inp +}
{+ directory: nmr_calc +}
{+ description: determine accepted structures and generate
ensemble averages +}
{+ authors: Gregory Warren, Michael Nilges, Axel Brunger +}
{+ copyright: Yale University +}
{- 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 reference coordinate file *}
{===>} pdb.in.file.1="shortcp12_extended.pdb";
{========================== 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);
{================== average and print selections =====================}
{* Select whether the average will be generated from either trial or
accepted structures and whether to print accepted structures. If
the input coor and output coor names are different then the
printing format is as follows: output coor = pdb.out.name + _#.pdb
otherwise output coor = pdb.out.name + _#.pdb
accepted = pdb.out.name + a_#.pdb *}
{* number of structures in the ensemble *}
{===>} pdb.end.count=25;
{* print accepted structures *}
{+ choice: true false +}
{===>} flg.print.accept=true;
{* Select to calculate an average structure for either the trial or
accepted structures. *}
{* calculate average values for the ensemble? *}
{+ choice: true false +}
{===>} flg.calc.ave.struct=true;
{* calculate an average for the accepted structures? If calculate an
average for accepted is false then an average for the trial
ensemble will be calculated. *}
{+ choice: true false +}
{===>} flg.calc.ave.accpt=true;
{* calculate average coordinates for the accepted structures?
False will print the average values to a text file *}
{+ choice: true false +}
{===>} flg.calc.coor.accpt=true;
{* minimize average coordinate? *}
{+ choice: true false +}
{===>} flg.min.ave.coor=true;
{* calculate a pairwise rmsd? *}
{+ choice: true false +}
{===>} flg.calc.ave.pair=true;
{* generate a rms difference plot table on a per residue basis? *}
{+ choice: true false +}
{===>} flg.plot.rms=true;
{====================== acceptance selections =========================}
{* Input acceptance criteria. All selections containing negative
values will be ignored, except for total energy and vdw energy. *}
{* select using total energy? *}
{+ choice: true false +}
{===>} nmr.ener.flag=true;
{* total energy cutoff value *}
{===>} nmr.ener.val=400;
{* select using bonds? *}
{+ choice: true false +}
{===>} nmr.bond.flag=false;
{* rmsd cutoff *}
{===>} nmr.bond.rms=0.01;
{* cutoff value *}
{===>} nmr.bond.cut=0.05;
{* number of violations *}
{===>} nmr.bond.viol=-1;
{* select using angles? *}
{+ choice: true false +}
{===>} nmr.angl.flag=false;
{* rmsd cutoff *}
{===>} nmr.angl.rms=1.0;
{* cutoff value *}
{===>} nmr.angl.cut=5.0;
{* number of violations *}
{===>} nmr.angl.viol=-1;
{* select using impropers? *}
{+ choice: true false +}
{===>} nmr.impr.flag=false;
{* rmsd cutoff *}
{===>} nmr.impr.rms=1.0;
{* cutoff value *}
{===>} nmr.impr.cut=5.0;
{* number of violations *}
{===>} nmr.impr.viol=-1;
{* select using dihedrals? *}
{+ choice: true false +}
{===>} nmr.dihe.flag=false;
{* rmsd cutoff *}
{===>} nmr.dihe.rms=1.0;
{* cutoff value *}
{===>} nmr.dihe.cut=30.0;
{* number of violations *}
{===>} nmr.dihe.viol=-1;
{* select using vdw? *}
{+ choice: true false +}
{===>} nmr.vdw.flag=false;
{* calculate vdw using repel or LJ? *}
{+ choice: "repel" "LJ" +}
{===>} nmr.vdw.repel="repel";
{* energy value *}
{===>} nmr.vdw.ener=0;
{* cutoff value *}
{===>} nmr.vdw.cut=1.6;
{* number of violations *}
{===>} nmr.vdw.viol=-1;
{* select using noes? *}
{+ choice: true false +}
{===>} nmr.noe.flag=false;
{* rmsd cutoff *}
{===>} nmr.noe.rms=-1;
{* cutoff value *}
{===>} nmr.noe.cut=0.5;
{* number of violations *}
{===>} nmr.noe.viol=0;
{* select using 3-bond homonuclear j-coupling? *}
{+ choice: true false +}
{===>} nmr.jcoup.flag=false;
{* rmsd cutoff *}
{===>} nmr.jcoup.rms=-1;
{* cutoff value *}
{===>} nmr.jcoup.cut=1.0;
{* number of violations *}
{===>} nmr.jcoup.viol=0;
{* select using 1-bond heteronuclear j-coupling? *}
{+ choice: true false +}
{===>} nmr.oneb.flag=false;
{* rmsd cutoff *}
{===>} nmr.oneb.rms=-1;
{* cutoff value *}
{===>} nmr.oneb.cut=1.0;
{* number of violations *}
{===>} nmr.oneb.viol=-1;
{* select using alpha and beta carbon chemical shifts? *}
{+ choice: true false +}
{===>} nmr.carb.flag=false;
{* rmsd cutoff for alpha *}
{===>} nmr.carb.rms.a=-1;
{* rmsd cutoff for beta *}
{===>} nmr.carb.rms.b=-1;
{* cutoff value *}
{===>} nmr.carb.cut=1.0;
{* number of violations *}
{===>} nmr.carb.viol=0;
{* select using proton chemical shifts? *}
{+ choice: true false +}
{===>} nmr.prot.flag=false;
{* rmsd cutoff *}
{===>} nmr.prot.rms=-1;
{* cutoff value *}
{===>} nmr.prot.cut=0.3;
{* number of violations *}
{===>} nmr.prot.viol=-1;
{* select using diffusion anisotropy restraints *}
{+ choice: true false +}
{===>} nmr.dani.flag=false;
{* rmsd cutoff *}
{===>} nmr.dani.rms=-1;
{* cutoff value *}
{===>} nmr.dani.cut=1.0;
{* number of violations *}
{===>} nmr.dani.viol=-1;
{* select using susceptibility anisotropy restraints *}
{+ choice: true false +}
{===>} nmr.sani.flag=false;
{* rmsd cutoff *}
{===>} nmr.sani.rms=-1;
{* cutoff value *}
{===>} nmr.sani.cut=1.0;
{* number of violations *}
{===>} nmr.sani.viol=-1;
{* select using dihedral angle restraints? *}
{+ choice: true false +}
{===>} nmr.cdih.flag=false;
{* rmsd cutoff *}
{===>} nmr.cdih.rms=-1;
{* cutoff value *}
{===>} nmr.cdih.cut=5.0;
{* number of violations *}
{===>} nmr.cdih.viol=0;
{* select using planarity restraints? *}
{+ choice: true false +}
{===>} nmr.plan.flag=false;
{* energy value *}
{===>} nmr.plan.ener=-1;
{* x rot cutoff *}
{===>} nmr.plan.x=-1;
{* y rot cutoff *}
{===>} nmr.plan.y=-1;
{* z rot cutoff *}
{===>} nmr.plan.z=-1;
{* select using NCS restraints? *}
{+ choice: true false +}
{===>} nmr.ncs.flag=false;
{* energy value *}
{===>} nmr.ncs.ener=-1;
{============================= 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";
{* noe force value *}
{===>} nmr.noe.force=75;
{======================== 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 *}
{* The potential for the glycine class must be multiple *}
{===>} nmr.jcoup.file.2="";
{* 3-bond J-coupling non-glycine potential *}
{+ 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";
{* dihedral angle restraints force value *}
{===>} nmr.cdih.force=200;
{* 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 $pscale *}
{===>} nmr.plan.scale=150;
{* NCS-restraints file *}
{* example is in inputs/xtal_data/eg1_ncs_restrain.dat *}
{===>} nmr.ncs.file="";
{======================== input/output files ==========================}
{* base name for input coordinate file(s) *}
{===>} pdb.in.name="shortcp12_noe5778_talos30";
{* base name for output coordinate file(s) *}
{===>} pdb.out.name="shortcp12_noe5778_talos30_400a";
{===========================================================================}
{ things below this line do not normally need to be changed }
{ except for the torsion angle topology setup if you have }
{ molecules other than protein or nucleic acid }
{===========================================================================}
) {- end block parameter definition -}
checkversion 1.2
evaluate ($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 (&pdb.in.file.1 # "") then
coor @@&pdb.in.file.1
else
evaluate ($temp_file = &pdb.in.name+"_1.pdb")
coor @@$temp_file
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 ( $log_level = verbose ) then
set message=normal echo=on end
else
set message=off echo=off end
end if
{- Read experimental data -}
@CNS_NMRMODULE:readdata ( nmr=&nmr;
flag=&flg;
output=$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)
@CNS_NMRMODULE:acceptinit ( ave=$ave;
ave2=$ave2;
ener1=$ener1;
ener2=$ener2;
flag=&flg;
nmr=&nmr; )
{- 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 = $SELECT)
if (&nmr.dani.axis = "harm") then
do (harmonic=20.0) (resid 500 and name OO)
do (harmonic=0.0) (resid 500 and name Z )
do (harmonic=0.0) (resid 500 and name X )
do (harmonic=0.0) (resid 500 and name Y )
do (harmonic=0.0) (not (resid 500))
restraints harmonic exponent=2 end
elseif (&nmr.sani.axis = "harm") then
do (harmonic=20.0) (resid 500 and name OO)
do (harmonic=0.0) (resid 500 and name Z )
do (harmonic=0.0) (resid 500 and name X )
do (harmonic=0.0) (resid 500 and name Y )
do (harmonic=0.0) (not (resid 500))
restraints harmonic exponent=2 end
end if
{- scaling of nmr restraint data -}
evaluate ($count = 1)
while (&exist%nmr.dani.file.$count=true) loop nloop
evaluate ($clsname = "D"+encode($count))
if (&nmr.dani.file.$count # "" ) then
dani
class $$clsname force &nmr.dani.force.finl.$count
end
end if
evaluate ($count = $count + 1)
end loop nloop
evaluate ($count = 1)
while (&exist%nmr.sani.file.$count=true) loop nloop
evaluate ($clsname = "S"+encode($count))
if (&nmr.sani.file.$count # "" ) then
sani
class $$clsname force &nmr.sani.force.finl.$count
end
end if
evaluate ($count = $count + 1)
end loop nloop
noe
scale * &nmr.noe.force
end
restraints dihedral
scale = &nmr.cdih.force
end
{- set reference coordinates -}
if (&pdb.in.file.1 # "") then
do (refx=x) ( all )
do (refy=y) ( all )
do (refz=z) ( all )
end if
{- Begin protocol to read in structures -- loop until done -}
while (&pdb.end.count > $nmr.counter) loop main
evaluate ($nmr.trial.count = $nmr.trial.count + 1)
evaluate ($input_coor = &pdb.in.name+"_"+encode($nmr.trial.count)+".pdb")
set remarks=reset end
coor @@$input_coor
if (&nmr.dani.axis = "fixed" ) then
fix
select=(resname ANI)
end
elseif (&nmr.sani.axis = "fixed" ) then
fix
select=(resname ANI)
end
end if
flags exclude *
include bond angl dihe impr vdw elec
noe coup oneb carb prot dani
sani cdih ncs plan harm end
if (&nmr.vdw.repel="repel") then
parameter
nbonds
repel=0.80
rexp=2 irexp=2 rcon=1.
nbxmod=3
wmin=&nmr.vdw.cut
cutnb=6.0 ctonnb=2.99 ctofnb=3.
end
end
else
parameter
nbonds
repel=0
nbxmod=5
wmin=&nmr.vdw.cut
tolerance=0.5
cutnb=11.5 ctonnb=9.5 ctofnb=10.5
rdie vswitch switch
end
end
end if
igroup interaction ( all ) ( all ) weights * 1 end end
@CNS_NMRMODULE:acceptprint ( ave=$ave;
ave2=$ave2;
ener1=$ener1;
ener2=$ener2;
flag=&flg;
md=&md;
nmr=&nmr;
num=$num;
output=$nmr;
pdb=&pdb; )
end loop main
@CNS_NMRMODULE:acceptavecalc ( ave=$ave;
ave2=$ave2;
ener1=$ener1;
ener2=$ener2;
flag=&flg;
md=&md;
nmr=&nmr;
num=$num;
output=$nmr;
pdb=&pdb; )
stop
Contact the webmaster for help, if required. Thursday, April 25, 2024 6:38:10 AM GMT (wattos1)