Sat Oct 8 19:46:38 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 19:46:39 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 611 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6228567 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -31.83800 17.99000 ymin,ymax (A): -24.59000 23.35700 zmin,zma (A): -12.49700 44.65900 x,y,z range (A): 49.82800 47.94700 57.15600 scale (grids/A): 0.6228567 object centre (A): -6.924001 -0.6164999 16.08100 number of atom coordinates read : 2585 total number of charged atoms : 2454 net assigned charge : 4.300008 assigned positive charge : 392.6040 centred at (gu) : 88.44722 89.16435 89.84054 assigned negative charge : -388.3046 centred at (gu) : 88.33050 89.20290 89.73653 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6765 nv = 96 ne = 84 npr = 52665 no. pairs analyzed = 52665 no. exposed pairs = 3074 no. arc points = 21724 no. surface atoms = 1038 nbur = 1547 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 344 mr = 3808 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 124 time to turn everything in is 0.3000000 number of dielectric boundary points 3258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2169 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8182 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8064676E-09 1.0918789E-08 midg,1,midg; midg,igrid,midg 8.0035667E-09 9.6257069E-10 1,midg,midg; igrid,midg,midg -6.6390866E-09 8.6989544E-09 gauss-seidel spectral radius is 0.9866487 estimated iterations to convergence 71 setup time was (sec) 0.6100000 now iterating at: 19:46:39 rms-change max change #iterations 0.1317599 18.22128 at 10iterations 1.2304579E-02 1.698231 at 20iterations 1.1792898E-03 0.1575203 at 30iterations 1.1934827E-04 1.7795563E-02 at 40iterations 1.3879125E-05 2.2888184E-03 at 50iterations finished qdiffx linear iterations at : 19:46:43 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 1.3879125E-05 2.2888184E-03 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.600000 DelPhi exited at 19:46:44 4.602u 0.404s 0:05.26 95.0% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 19:46:44 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 611 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.868570 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -31.83800 17.99000 ymin,ymax (A): -24.59000 23.35700 zmin,zma (A): -12.49700 44.65900 x,y,z range (A): 49.82800 47.94700 57.15600 scale (grids/A): 1.868570 object centre (A): -6.924001 -0.6164999 16.08100 number of atom coordinates read : 2585 total number of charged atoms : 2454 net assigned charge : 4.300008 assigned positive charge : 392.6040 centred at (gu) : 85.34142 87.49269 89.52115 assigned negative charge : -388.3046 centred at (gu) : 84.99149 87.60858 89.20942 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73032 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21724 grid for indexing accessible points = 1.400000 m= 26444 mr = 51262 m= 3917 mr = 19810 m= 222 mr = 2545 m= 2 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 3853 time to turn everything in is 0.5900000 number of dielectric boundary points 29915 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19282 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.6228567 object centre at (A) : -6.924001 -0.6164999 16.08100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1035921E-02 2.3662662E-02 midg,1,midg; midg,igrid,midg 1.5005629E-02 5.4992470E-03 1,midg,midg; igrid,midg,midg -5.9843585E-03 3.6374319E-02 gauss-seidel spectral radius is 0.9985817 estimated iterations to convergence 210 setup time was (sec) 0.8800000 now iterating at: 19:46:45 rms-change max change #iterations 4.047430 168.0520 at 10iterations 1.871449 64.68965 at 20iterations 0.8611424 31.71195 at 30iterations 0.3965067 12.15842 at 40iterations 0.1833253 6.807425 at 50iterations 8.4845826E-02 2.566118 at 60iterations 3.9095346E-02 1.288857 at 70iterations 1.8142171E-02 0.5807343 at 80iterations 8.3442666E-03 0.2842197 at 90iterations 3.8439997E-03 0.1215715 at 100iterations 1.7791963E-03 6.3095093E-02 at 110iterations 8.2528079E-04 2.7719021E-02 at 120iterations finished qdiffx linear iterations at : 19:46:55 total time elapsed so far: 10.86000 # loops : 120 mean,max change (kT/e) : 8.2528079E-04 2.7719021E-02 energy calculations done at 10.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.02000 DelPhi exited at 19:46:56 11.027u 0.447s 0:11.76 97.4% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Sat Oct 8 2011 at 19:46:56 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2585 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 611 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.802855 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -31.83800 17.99000 ymin,ymax (A): -24.59000 23.35700 zmin,zma (A): -12.49700 44.65900 x,y,z range (A): 49.82800 47.94700 57.15600 scale (grids/A): 2.802855 object centre (A): -6.924001 -0.6164999 16.08100 number of atom coordinates read : 2585 total number of charged atoms : 2454 net assigned charge : 4.300008 assigned positive charge : 392.6040 centred at (gu) : 83.01208 86.23874 89.28156 assigned negative charge : -388.3046 centred at (gu) : 82.48726 86.41268 88.81414 start vw surface at 0.1100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 168899 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21724 grid for indexing accessible points = 1.400000 m= 86554 mr = 123984 m= 30514 mr = 71670 m= 7095 mr = 24765 m= 895 mr = 5496 m= 56 mr = 619 m= 0 mr = 26 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 13056 time to turn everything in is 1.520000 number of dielectric boundary points 67453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 19627 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.868570 object centre at (A) : -6.924001 -0.6164999 16.08100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4978227E-03 0.2249682 midg,1,midg; midg,igrid,midg 0.1916802 7.8582399E-02 1,midg,midg; igrid,midg,midg -4.0208641E-02 0.4714354 gauss-seidel spectral radius is 0.9992399 estimated iterations to convergence 286 setup time was (sec) 1.850000 now iterating at: 19:46:58 rms-change max change #iterations 9.622361 363.8469 at 10iterations 5.544290 128.9204 at 20iterations 3.175733 69.16287 at 30iterations 1.814972 40.04501 at 40iterations 1.037830 24.76289 at 50iterations 0.5927780 12.04719 at 60iterations 0.3391246 6.417587 at 70iterations 0.1933746 3.817127 at 80iterations 0.1101214 2.464678 at 90iterations 6.2999621E-02 1.111910 at 100iterations 3.5963904E-02 0.6784310 at 110iterations 2.0502947E-02 0.4218445 at 120iterations 1.1662741E-02 0.2289724 at 130iterations 6.6711549E-03 0.1267624 at 140iterations 3.8151937E-03 7.4048996E-02 at 150iterations 2.1790024E-03 4.1257381E-02 at 160iterations 1.2503974E-03 2.5947571E-02 at 170iterations 7.2365225E-04 1.4176846E-02 at 180iterations finished qdiffx linear iterations at : 19:47:14 total time elapsed so far: 17.75000 # loops : 180 mean,max change (kT/e) : 7.2365225E-04 1.4176846E-02 energy calculations done at 17.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.91000 DelPhi exited at 19:47:14 17.919u 0.460s 0:18.65 98.4% 0+0k 0+0io 0pf+0w