Tue Oct 11 08:32:57 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 08:32:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7063492 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): -20.55900 29.84100 ymin,ymax (A): -11.85200 30.70700 zmin,zma (A): -8.630000 38.44100 x,y,z range (A): 50.40000 42.55900 47.07100 scale (grids/A): 0.7063492 object centre (A): 4.641000 9.427500 14.90550 number of atom coordinates read : 2047 total number of charged atoms : 1919 net assigned charge : 6.500009 assigned positive charge : 310.0089 centred at (gu) : 90.92393 89.87489 90.99557 assigned negative charge : -303.5092 centred at (gu) : 90.87145 89.80366 90.88490 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7016 nv = 96 ne = 84 npr = 40681 no. pairs analyzed = 40681 no. exposed pairs = 2539 no. arc points = 17417 no. surface atoms = 852 nbur = 1195 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 467 mr = 4003 m= 0 mr = 96 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1646 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7750 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.4653349E-10 1.2621842E-07 midg,1,midg; midg,igrid,midg 1.9381757E-08 8.3738819E-08 1,midg,midg; igrid,midg,midg 2.3688308E-08 9.2139487E-08 gauss-seidel spectral radius is 0.9895511 estimated iterations to convergence 80 setup time was (sec) 0.4900000 now iterating at: 08:32:57 rms-change max change #iterations 0.1935776 24.57839 at 10iterations 2.3725148E-02 3.863636 at 20iterations 3.0697472E-03 0.4068451 at 30iterations 4.8321122E-04 6.4770699E-02 at 40iterations 1.1571384E-04 1.3959885E-02 at 50iterations finished qdiffx linear iterations at : 08:33:00 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.1571384E-04 1.3959885E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 08:33:00 3.343u 0.150s 0:03.80 91.8% 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 08:33:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 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: 2.119048 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): -20.55900 29.84100 ymin,ymax (A): -11.85200 30.70700 zmin,zma (A): -8.630000 38.44100 x,y,z range (A): 50.40000 42.55900 47.07100 scale (grids/A): 2.119048 object centre (A): 4.641000 9.427500 14.90550 number of atom coordinates read : 2047 total number of charged atoms : 1919 net assigned charge : 6.500009 assigned positive charge : 310.0089 centred at (gu) : 92.77177 89.62457 92.98676 assigned negative charge : -303.5092 centred at (gu) : 92.61433 89.41105 92.65480 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17417 grid for indexing accessible points = 1.400000 m= 30160 mr = 52349 m= 5746 mr = 23015 m= 507 mr = 3806 m= 16 mr = 277 m= 0 mr = 3 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 31112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 15249 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) : 0.7063492 object centre at (A) : 4.641000 9.427500 14.90550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.2570940E-02 3.5768859E-02 midg,1,midg; midg,igrid,midg 2.0746542E-02 2.0838421E-02 1,midg,midg; igrid,midg,midg 5.8898676E-02 3.1757697E-02 gauss-seidel spectral radius is 0.9988275 estimated iterations to convergence 231 setup time was (sec) 0.8600000 now iterating at: 08:33:01 rms-change max change #iterations 4.546831 180.6984 at 10iterations 2.246495 71.84265 at 20iterations 1.114275 35.98754 at 30iterations 0.5520155 15.87183 at 40iterations 0.2729541 8.309536 at 50iterations 0.1356592 4.141221 at 60iterations 6.7612655E-02 2.097344 at 70iterations 3.3465061E-02 1.008101 at 80iterations 1.6595278E-02 0.5060501 at 90iterations 8.3323177E-03 0.2478914 at 100iterations 4.1633788E-03 0.1246037 at 110iterations 2.1193775E-03 7.4924469E-02 at 120iterations finished qdiffx linear iterations at : 08:33:08 total time elapsed so far: 7.380000 # loops : 120 mean,max change (kT/e) : 2.1193775E-03 7.4924469E-02 energy calculations done at 7.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 08:33:09 7.568u 0.181s 0:08.51 90.9% 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 08:33:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2047 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.178571 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): -20.55900 29.84100 ymin,ymax (A): -11.85200 30.70700 zmin,zma (A): -8.630000 38.44100 x,y,z range (A): 50.40000 42.55900 47.07100 scale (grids/A): 3.178571 object centre (A): 4.641000 9.427500 14.90550 number of atom coordinates read : 2047 total number of charged atoms : 1919 net assigned charge : 6.500009 assigned positive charge : 310.0089 centred at (gu) : 94.15764 89.43673 94.48014 assigned negative charge : -303.5092 centred at (gu) : 93.92175 89.11658 93.98225 start vw surface at 0.1400000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 170677 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17417 grid for indexing accessible points = 1.400000 m= 93578 mr = 125858 m= 38383 mr = 77969 m= 10714 mr = 31653 m= 2100 mr = 8318 m= 236 mr = 1544 m= 15 mr = 172 m= 0 mr = 4 time to grow re-entrant surface = 0.9200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 70185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 15352 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) : 2.119048 object centre at (A) : 4.641000 9.427500 14.90550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3795720 0.3099558 midg,1,midg; midg,igrid,midg 0.1557404 0.1150642 1,midg,midg; igrid,midg,midg 0.4735315 0.1279600 gauss-seidel spectral radius is 0.9992948 estimated iterations to convergence 297 setup time was (sec) 2.160000 now iterating at: 08:33:11 rms-change max change #iterations 10.09109 405.3598 at 10iterations 5.939230 121.7776 at 20iterations 3.504379 68.08987 at 30iterations 2.060001 40.57468 at 40iterations 1.209160 23.38249 at 50iterations 0.7105400 13.88564 at 60iterations 0.4160593 9.705666 at 70iterations 0.2442807 4.260383 at 80iterations 0.1426900 2.352160 at 90iterations 8.3708681E-02 1.559845 at 100iterations 4.9225148E-02 0.8947630 at 110iterations 2.8947087E-02 0.5767441 at 120iterations 1.7180124E-02 0.3847485 at 130iterations 1.0339360E-02 0.1962802 at 140iterations 6.3966946E-03 0.1391487 at 150iterations 4.1052303E-03 8.1932068E-02 at 160iterations 2.7871518E-03 5.2064896E-02 at 170iterations 2.0117641E-03 4.0069580E-02 at 180iterations finished qdiffx linear iterations at : 08:33:22 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 2.0117641E-03 4.0069580E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 08:33:23 12.969u 0.223s 0:13.59 96.9% 0+0k 0+0io 0pf+0w