Mon Oct 10 17:03:48 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 Mon Oct 10 2011 at 17:03:48 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2575 !!! WARNING: ADP 535 has a net charge of -2.0000 !!! WARNING: MG7 702 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6151081 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): 11.20400 61.01000 ymin,ymax (A): 8.513000 56.88600 zmin,zma (A): 9.273999 67.15000 x,y,z range (A): 49.80600 48.37300 57.87600 scale (grids/A): 0.6151081 object centre (A): 36.10700 32.69950 38.21200 number of atom coordinates read : 2575 total number of charged atoms : 2439 net assigned charge : 2.900012 assigned positive charge : 387.3328 centred at (gu) : 90.08702 89.55787 89.20715 assigned negative charge : -384.4335 centred at (gu) : 90.01652 89.58659 89.32194 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6575 nv = 96 ne = 84 npr = 52217 no. pairs analyzed = 52217 no. exposed pairs = 3329 no. arc points = 23479 no. surface atoms = 1122 nbur = 1453 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 328 mr = 3462 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2372 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8043 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0045984E-08 -3.9100407E-09 midg,1,midg; midg,igrid,midg 3.9421999E-09 2.7922906E-10 1,midg,midg; igrid,midg,midg -2.0697501E-09 6.0500502E-09 gauss-seidel spectral radius is 0.9863197 estimated iterations to convergence 70 setup time was (sec) 0.3900000 now iterating at: 17:03:49 rms-change max change #iterations 0.1234630 19.93697 at 10iterations 1.1479737E-02 1.807955 at 20iterations 1.0891507E-03 0.1804457 at 30iterations 1.2734496E-04 2.0151138E-02 at 40iterations 2.3183758E-05 4.4021606E-03 at 50iterations finished qdiffx linear iterations at : 17:03:52 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 2.3183758E-05 4.4021606E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 17:03:53 3.528u 0.214s 0:04.91 75.9% 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 Mon Oct 10 2011 at 17:03:53 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2575 !!! WARNING: ADP 535 has a net charge of -2.0000 !!! WARNING: MG7 702 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.845324 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): 11.20400 61.01000 ymin,ymax (A): 8.513000 56.88600 zmin,zma (A): 9.273999 67.15000 x,y,z range (A): 49.80600 48.37300 57.87600 scale (grids/A): 1.845324 object centre (A): 36.10700 32.69950 38.21200 number of atom coordinates read : 2575 total number of charged atoms : 2439 net assigned charge : 2.900012 assigned positive charge : 387.3328 centred at (gu) : 90.26065 88.67316 87.62092 assigned negative charge : -384.4335 centred at (gu) : 90.04928 88.75953 87.96564 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23479 grid for indexing accessible points = 1.400000 m= 24907 mr = 48315 m= 3575 mr = 18125 m= 179 mr = 2165 m= 1 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1660 time to turn everything in is 0.3700000 number of dielectric boundary points 31167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 19141 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) : 0.6151081 object centre at (A) : 36.10700 32.69950 38.21200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5799675E-02 -1.9016195E-02 midg,1,midg; midg,igrid,midg 1.2825508E-02 1.7249659E-02 1,midg,midg; igrid,midg,midg -9.9027865E-03 3.5431939E-03 gauss-seidel spectral radius is 0.9985532 estimated iterations to convergence 208 setup time was (sec) 0.6600000 now iterating at: 17:03:54 rms-change max change #iterations 4.033388 197.3298 at 10iterations 1.839776 62.97965 at 20iterations 0.8418534 26.56607 at 30iterations 0.3851711 13.80680 at 40iterations 0.1768343 6.142178 at 50iterations 8.0881767E-02 2.559530 at 60iterations 3.7068762E-02 1.166311 at 70iterations 1.6964542E-02 0.5631371 at 80iterations 7.7740368E-03 0.2551880 at 90iterations 3.5850948E-03 0.1161816 at 100iterations 1.6522236E-03 5.7197571E-02 at 110iterations 7.6946552E-04 2.7551651E-02 at 120iterations finished qdiffx linear iterations at : 17:04:06 total time elapsed so far: 8.650000 # loops : 120 mean,max change (kT/e) : 7.6946552E-04 2.7551651E-02 energy calculations done at 8.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.780000 DelPhi exited at 17:04:07 8.784u 0.301s 0:14.08 64.4% 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 Mon Oct 10 2011 at 17:04:08 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2575 !!! WARNING: ADP 535 has a net charge of -2.0000 !!! WARNING: MG7 702 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.767987 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): 11.20400 61.01000 ymin,ymax (A): 8.513000 56.88600 zmin,zma (A): 9.273999 67.15000 x,y,z range (A): 49.80600 48.37300 57.87600 scale (grids/A): 2.767987 object centre (A): 36.10700 32.69950 38.21200 number of atom coordinates read : 2575 total number of charged atoms : 2439 net assigned charge : 2.900012 assigned positive charge : 387.3328 centred at (gu) : 90.39092 88.00968 86.43110 assigned negative charge : -384.4335 centred at (gu) : 90.07391 88.13927 86.94845 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 164956 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23479 grid for indexing accessible points = 1.400000 m= 81262 mr = 117770 m= 28427 mr = 65744 m= 6228 mr = 22724 m= 729 mr = 4565 m= 21 mr = 477 m= 0 mr = 6 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 5559 time to turn everything in is 0.9200000 number of dielectric boundary points 70337 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19511 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) : 1.845324 object centre at (A) : 36.10700 32.69950 38.21200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6536556 -0.1649397 midg,1,midg; midg,igrid,midg 0.1024069 0.2210542 1,midg,midg; igrid,midg,midg -0.1651127 3.0069528E-02 gauss-seidel spectral radius is 0.9992421 estimated iterations to convergence 287 setup time was (sec) 1.170000 now iterating at: 17:04:10 rms-change max change #iterations 9.532395 331.4424 at 10iterations 5.516512 160.5367 at 20iterations 3.173925 70.68153 at 30iterations 1.821804 37.60081 at 40iterations 1.044075 19.67883 at 50iterations 0.5980771 11.50357 at 60iterations 0.3414391 7.650570 at 70iterations 0.1948787 4.212488 at 80iterations 0.1112026 2.419193 at 90iterations 6.3443698E-02 1.295731 at 100iterations 3.6293991E-02 0.6957417 at 110iterations 2.0638321E-02 0.3696518 at 120iterations 1.1804113E-02 0.2275200 at 130iterations 6.7294515E-03 0.1239266 at 140iterations 3.8445345E-03 7.3736191E-02 at 150iterations 2.2012682E-03 4.1824341E-02 at 160iterations 1.2638058E-03 2.3562193E-02 at 170iterations 7.3035248E-04 1.3533592E-02 at 180iterations finished qdiffx linear iterations at : 17:04:22 total time elapsed so far: 13.39000 # loops : 180 mean,max change (kT/e) : 7.3035248E-04 1.3533592E-02 energy calculations done at 13.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.53000 DelPhi exited at 17:04:23 13.529u 0.229s 0:14.50 94.7% 0+0k 0+0io 0pf+0w