Tue Oct 11 03:40:50 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+sph.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 = amb.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 Tue Oct 11 2011 at 03:40:50 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2802 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6352832 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): -10.93600 36.99300 ymin,ymax (A): -26.93700 23.34700 zmin,zma (A): -10.76300 45.27500 x,y,z range (A): 47.92900 50.28400 56.03800 scale (grids/A): 0.6352832 object centre (A): 13.02850 -1.795000 17.25600 number of atom coordinates read : 2802 total number of charged atoms : 2649 net assigned charge : 2.140018 assigned positive charge : 424.4696 centred at (gu) : 89.92640 90.08009 91.91656 assigned negative charge : -422.3302 centred at (gu) : 89.69994 89.97071 91.88258 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7395 nv = 96 ne = 84 npr = 57450 no. pairs analyzed = 57450 no. exposed pairs = 3359 no. arc points = 23137 no. surface atoms = 1127 nbur = 1675 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 358 mr = 4168 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3200000 number of dielectric boundary points 3538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2308 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9060 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9479533E-10 9.7635313E-09 midg,1,midg; midg,igrid,midg -9.4544710E-09 1.4942477E-08 1,midg,midg; igrid,midg,midg -2.3503814E-08 2.6789252E-08 gauss-seidel spectral radius is 0.9871742 estimated iterations to convergence 72 setup time was (sec) 0.6200000 now iterating at: 03:40:51 rms-change max change #iterations 0.1446501 20.56486 at 10iterations 1.4176086E-02 1.927393 at 20iterations 1.4197215E-03 0.2387590 at 30iterations 1.5276406E-04 2.2014618E-02 at 40iterations 2.0508198E-05 2.8152466E-03 at 50iterations finished qdiffx linear iterations at : 03:40:55 total time elapsed so far: 4.330000 # loops : 50 mean,max change (kT/e) : 2.0508198E-05 2.8152466E-03 energy calculations done at 4.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.500000 DelPhi exited at 03:40:56 4.504u 0.397s 0:05.56 87.9% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 03:40:56 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2802 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.905850 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): -10.93600 36.99300 ymin,ymax (A): -26.93700 23.34700 zmin,zma (A): -10.76300 45.27500 x,y,z range (A): 47.92900 50.28400 56.03800 scale (grids/A): 1.905850 object centre (A): 13.02850 -1.795000 17.25600 number of atom coordinates read : 2802 total number of charged atoms : 2649 net assigned charge : 2.140018 assigned positive charge : 424.4696 centred at (gu) : 89.77892 90.23971 95.74911 assigned negative charge : -422.3302 centred at (gu) : 89.09922 89.91177 95.64722 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 80254 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23137 grid for indexing accessible points = 1.400000 m= 28301 mr = 56772 m= 4087 mr = 20919 m= 205 mr = 2496 m= 2 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1922 time to turn everything in is 0.6400000 number of dielectric boundary points 32577 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 20797 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) : 0.6352832 object centre at (A) : 13.02850 -1.795000 17.25600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6512876E-02 4.1752099E-03 midg,1,midg; midg,igrid,midg -1.4197410E-02 -3.7326298E-03 1,midg,midg; igrid,midg,midg -9.5589822E-03 4.8876740E-02 gauss-seidel spectral radius is 0.9986516 estimated iterations to convergence 216 setup time was (sec) 0.9400000 now iterating at: 03:40:57 rms-change max change #iterations 4.461036 188.8746 at 10iterations 2.100222 73.52875 at 20iterations 0.9923040 32.37129 at 30iterations 0.4693032 14.52421 at 40iterations 0.2211125 6.722288 at 50iterations 0.1042881 3.197638 at 60iterations 4.9212694E-02 1.823880 at 70iterations 2.3106804E-02 0.6786737 at 80iterations 1.0942055E-02 0.3421721 at 90iterations 5.1566600E-03 0.1652718 at 100iterations 2.4334469E-03 7.4365616E-02 at 110iterations 1.1533767E-03 3.3905029E-02 at 120iterations finished qdiffx linear iterations at : 03:41:07 total time elapsed so far: 10.51000 # loops : 120 mean,max change (kT/e) : 1.1533767E-03 3.3905029E-02 energy calculations done at 10.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.67000 DelPhi exited at 03:41:07 10.678u 0.439s 0:11.40 97.3% 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 Tue Oct 11 2011 at 03:41:07 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2802 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.858774 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): -10.93600 36.99300 ymin,ymax (A): -26.93700 23.34700 zmin,zma (A): -10.76300 45.27500 x,y,z range (A): 47.92900 50.28400 56.03800 scale (grids/A): 2.858774 object centre (A): 13.02850 -1.795000 17.25600 number of atom coordinates read : 2802 total number of charged atoms : 2649 net assigned charge : 2.140018 assigned positive charge : 424.4696 centred at (gu) : 89.66824 90.35937 98.62341 assigned negative charge : -422.3302 centred at (gu) : 88.64880 89.86763 98.47077 start vw surface at 0.1300000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 185721 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23137 grid for indexing accessible points = 1.400000 m= 93250 mr = 137421 m= 32045 mr = 76627 m= 7302 mr = 25710 m= 960 mr = 5537 m= 54 mr = 636 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 6644 time to turn everything in is 1.720000 number of dielectric boundary points 73372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 21188 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) : 1.905850 object centre at (A) : 13.02850 -1.795000 17.25600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5366183 0.2534145 midg,1,midg; midg,igrid,midg -0.1862016 -0.1365724 1,midg,midg; igrid,midg,midg -4.0276125E-02 0.4499720 gauss-seidel spectral radius is 0.9992626 estimated iterations to convergence 291 setup time was (sec) 2.040000 now iterating at: 03:41:10 rms-change max change #iterations 10.33546 349.8323 at 10iterations 6.031767 131.6186 at 20iterations 3.512773 75.20022 at 30iterations 2.035569 38.03326 at 40iterations 1.180361 21.46286 at 50iterations 0.6824370 12.92739 at 60iterations 0.3940528 7.030628 at 70iterations 0.2276913 4.883918 at 80iterations 0.1314999 2.459549 at 90iterations 7.5732574E-02 1.397541 at 100iterations 4.3780185E-02 0.7940655 at 110iterations 2.5245836E-02 0.4754925 at 120iterations 1.4535800E-02 0.2585192 at 130iterations 8.3912946E-03 0.1521530 at 140iterations 4.8453482E-03 8.9763641E-02 at 150iterations 2.8187109E-03 4.6325684E-02 at 160iterations 1.6385757E-03 2.8167725E-02 at 170iterations 9.6008717E-04 1.6786575E-02 at 180iterations finished qdiffx linear iterations at : 03:41:26 total time elapsed so far: 17.93000 # loops : 180 mean,max change (kT/e) : 9.6008717E-04 1.6786575E-02 energy calculations done at 17.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.09000 DelPhi exited at 03:41:26 18.094u 0.460s 0:18.87 98.3% 0+0k 0+0io 0pf+0w