Sat Oct 8 19:32:29 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 19:32:29 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 507 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6901900 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): -7.768000 42.15800 ymin,ymax (A): -4.750000 46.83000 zmin,zma (A): -8.175000 40.73700 x,y,z range (A): 49.92600 51.58000 48.91200 scale (grids/A): 0.6901900 object centre (A): 17.19500 21.04000 16.28100 number of atom coordinates read : 2579 total number of charged atoms : 2475 net assigned charge : 4.500006 assigned positive charge : 395.4670 centred at (gu) : 88.57185 92.08006 90.66548 assigned negative charge : -390.9676 centred at (gu) : 88.45687 92.19081 90.59888 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8284 nv = 96 ne = 84 npr = 53096 no. pairs analyzed = 53096 no. exposed pairs = 3010 no. arc points = 21773 no. surface atoms = 1011 nbur = 1568 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 526 mr = 4769 m= 2 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 152 time to turn everything in is 0.3500000 number of dielectric boundary points 3937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1994 ## 185 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9574 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.2434388E-10 6.1593219E-08 midg,1,midg; midg,igrid,midg 4.7692982E-08 -3.1546886E-08 1,midg,midg; igrid,midg,midg -2.9667335E-08 5.5461790E-08 gauss-seidel spectral radius is 0.9891114 estimated iterations to convergence 78 setup time was (sec) 0.6300000 now iterating at: 19:32:30 rms-change max change #iterations 0.2053181 31.05121 at 10iterations 2.3938544E-02 3.423994 at 20iterations 2.7996991E-03 0.3710747 at 30iterations 3.2706960E-04 4.3174744E-02 at 40iterations 3.8856011E-05 4.8179626E-03 at 50iterations finished qdiffx linear iterations at : 19:32:33 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 3.8856011E-05 4.8179626E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 19:32:34 4.068u 0.260s 0:04.60 93.9% 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 Sat Oct 8 2011 at 19:32:34 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 507 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.070570 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): -7.768000 42.15800 ymin,ymax (A): -4.750000 46.83000 zmin,zma (A): -8.175000 40.73700 x,y,z range (A): 49.92600 51.58000 48.91200 scale (grids/A): 2.070570 object centre (A): 17.19500 21.04000 16.28100 number of atom coordinates read : 2579 total number of charged atoms : 2475 net assigned charge : 4.500006 assigned positive charge : 395.4670 centred at (gu) : 85.71492 96.23978 91.99581 assigned negative charge : -390.9676 centred at (gu) : 85.37032 96.57228 91.79638 start vw surface at 0.1600000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 88332 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21773 grid for indexing accessible points = 1.400000 m= 34783 mr = 62648 m= 6643 mr = 26846 m= 594 mr = 4594 m= 5 mr = 319 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 5608 time to turn everything in is 0.7900000 number of dielectric boundary points 35950 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.9400000 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) : 0.6901900 object centre at (A) : 17.19500 21.04000 16.28100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1582047E-02 3.1548038E-02 midg,1,midg; midg,igrid,midg -2.9211858E-04 -2.1943718E-02 1,midg,midg; igrid,midg,midg -9.0564936E-03 9.4766796E-02 gauss-seidel spectral radius is 0.9988252 estimated iterations to convergence 231 setup time was (sec) 1.100000 now iterating at: 19:32:35 rms-change max change #iterations 5.018347 190.9354 at 10iterations 2.462329 77.74127 at 20iterations 1.215220 34.79545 at 30iterations 0.6016638 18.41684 at 40iterations 0.2990018 8.259739 at 50iterations 0.1471177 4.386491 at 60iterations 7.2953582E-02 1.975938 at 70iterations 3.6100630E-02 1.079750 at 80iterations 1.7867880E-02 0.4915466 at 90iterations 8.8426378E-03 0.2616348 at 100iterations 4.3753693E-03 0.1250496 at 110iterations 2.1647890E-03 7.3625565E-02 at 120iterations finished qdiffx linear iterations at : 19:32:44 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 2.1647890E-03 7.3625565E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.640000 DelPhi exited at 19:32:44 9.644u 0.273s 0:10.18 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 Sat Oct 8 2011 at 19:32:44 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 507 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.105855 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): -7.768000 42.15800 ymin,ymax (A): -4.750000 46.83000 zmin,zma (A): -8.175000 40.73700 x,y,z range (A): 49.92600 51.58000 48.91200 scale (grids/A): 3.105855 object centre (A): 17.19500 21.04000 16.28100 number of atom coordinates read : 2579 total number of charged atoms : 2475 net assigned charge : 4.500006 assigned positive charge : 395.4670 centred at (gu) : 83.57217 99.35951 92.99362 assigned negative charge : -390.9676 centred at (gu) : 83.05543 99.85833 92.69445 start vw surface at 0.1500000 fill in re-entrant regions at 1.130000 boundary points on vw surface= 203800 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21773 grid for indexing accessible points = 1.400000 m= 108906 mr = 150559 m= 43909 mr = 91570 m= 12569 mr = 36568 m= 2489 mr = 9985 m= 238 mr = 1937 m= 6 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 1.250000 no. cavity mid-points inaccessible to solvent = 18781 time to turn everything in is 2.530000 number of dielectric boundary points 81147 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.680000 number of grid points assigned charge 19799 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) : 2.070570 object centre at (A) : 17.19500 21.04000 16.28100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2966470 0.2120663 midg,1,midg; midg,igrid,midg -0.1454553 -0.2650656 1,midg,midg; igrid,midg,midg -0.1346111 1.404209 gauss-seidel spectral radius is 0.9993017 estimated iterations to convergence 299 setup time was (sec) 2.850000 now iterating at: 19:32:47 rms-change max change #iterations 11.12951 405.7977 at 10iterations 6.509186 141.0143 at 20iterations 3.808471 69.92651 at 30iterations 2.232329 38.98333 at 40iterations 1.304056 19.51460 at 50iterations 0.7624506 13.46910 at 60iterations 0.4450582 6.795578 at 70iterations 0.2600188 4.331982 at 80iterations 0.1515891 2.522857 at 90iterations 8.8563040E-02 1.443176 at 100iterations 5.1786155E-02 0.8133907 at 110iterations 3.0171439E-02 0.5971680 at 120iterations 1.7598724E-02 0.2887403 at 130iterations 1.0277162E-02 0.1636047 at 140iterations 5.9890719E-03 0.1014032 at 150iterations 3.5080588E-03 5.7505608E-02 at 160iterations 2.0492631E-03 4.2240143E-02 at 170iterations 1.2009282E-03 1.9470215E-02 at 180iterations finished qdiffx linear iterations at : 19:33:01 total time elapsed so far: 16.74000 # loops : 180 mean,max change (kT/e) : 1.2009282E-03 1.9470215E-02 energy calculations done at 16.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.92000 DelPhi exited at 19:33:02 16.921u 0.325s 0:17.54 98.2% 0+0k 0+0io 0pf+0w