Tue Oct 11 08:41:33 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 Tue Oct 11 2011 at 08:41:33 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1076 !!! WARNING: GLM 319 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.9999998E-03 grid size : 179 scale,in grids/A, set to be: 0.8101588 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): 81.72400 121.1270 ymin,ymax (A): 73.41800 105.1280 zmin,zma (A): 36.03000 79.97200 x,y,z range (A): 39.40300 31.71000 43.94200 scale (grids/A): 0.8101588 object centre (A): 101.4255 89.27299 58.00100 number of atom coordinates read : 1076 total number of charged atoms : 941 net assigned charge : 0.1340044 assigned positive charge : 150.1141 centred at (gu) : 90.28872 88.93104 89.33327 assigned negative charge : -149.9801 centred at (gu) : 90.45178 88.73054 89.29353 start vw surface at 5.9999999E-02 fill in re-entrant regions at 5.9999999E-02 boundary points on vw surface= 4833 nv = 96 ne = 84 npr = 22112 no. pairs analyzed = 22112 no. exposed pairs = 1415 no. arc points = 10601 no. surface atoms = 474 nbur = 602 mkacc time = 4.0000003E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 369 mr = 2447 m= 4 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 5.0000001E-02 no. cavity mid-points inaccessible to solvent = 74 time to turn everything in is 0.1100000 number of dielectric boundary points 2680 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 660 ## 52 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 4463 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1124823E-08 7.5995246E-08 midg,1,midg; midg,igrid,midg -4.1515113E-07 2.9994465E-07 1,midg,midg; igrid,midg,midg 2.8342234E-07 -2.8934724E-07 gauss-seidel spectral radius is 0.9919423 estimated iterations to convergence 90 setup time was (sec) 0.3000000 now iterating at: 08:41:34 rms-change max change #iterations 0.2424581 37.45272 at 10iterations 3.8123649E-02 6.132406 at 20iterations 5.9520155E-03 0.8907013 at 30iterations 9.2587224E-04 0.1387444 at 40iterations 1.4678940E-04 2.1739960E-02 at 50iterations finished qdiffx linear iterations at : 08:41:37 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.4678940E-04 2.1739960E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 08:41:37 3.317u 0.183s 0:03.92 89.0% 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 Tue Oct 11 2011 at 08:41:37 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1076 !!! WARNING: GLM 319 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.430476 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): 81.72400 121.1270 ymin,ymax (A): 73.41800 105.1280 zmin,zma (A): 36.03000 79.97200 x,y,z range (A): 39.40300 31.71000 43.94200 scale (grids/A): 2.430476 object centre (A): 101.4255 89.27299 58.00100 number of atom coordinates read : 1076 total number of charged atoms : 941 net assigned charge : 0.1340044 assigned positive charge : 150.1141 centred at (gu) : 90.86636 86.79332 88.00011 assigned negative charge : -149.9801 centred at (gu) : 91.35548 86.19153 87.88065 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 49620 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10601 grid for indexing accessible points = 1.400000 m= 19119 mr = 31909 m= 4595 mr = 14085 m= 657 mr = 3166 m= 52 mr = 418 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 2212 time to turn everything in is 0.2800000 number of dielectric boundary points 24442 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 7513 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) : 0.8101588 object centre at (A) : 101.4255 89.27299 58.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0914426E-02 8.4428629E-03 midg,1,midg; midg,igrid,midg 2.4258909E-03 3.1554937E-02 1,midg,midg; igrid,midg,midg 1.9371463E-02 -2.9875418E-02 gauss-seidel spectral radius is 0.9989835 estimated iterations to convergence 248 setup time was (sec) 0.4900000 now iterating at: 08:41:38 rms-change max change #iterations 3.971038 238.7750 at 10iterations 2.046849 85.84218 at 20iterations 1.066435 37.69609 at 30iterations 0.5488126 19.00090 at 40iterations 0.2848995 9.645676 at 50iterations 0.1475841 4.893457 at 60iterations 7.6762475E-02 2.670635 at 70iterations 3.9663259E-02 1.379382 at 80iterations 2.0553144E-02 0.6798735 at 90iterations 1.0650171E-02 0.3777742 at 100iterations 5.5288570E-03 0.2178497 at 110iterations 2.8727222E-03 0.1002426 at 120iterations finished qdiffx linear iterations at : 08:41:45 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 2.8727222E-03 0.1002426 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 08:41:45 7.614u 0.189s 0:08.12 95.9% 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 08:41:45 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1076 !!! WARNING: GLM 319 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.645715 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): 81.72400 121.1270 ymin,ymax (A): 73.41800 105.1280 zmin,zma (A): 36.03000 79.97200 x,y,z range (A): 39.40300 31.71000 43.94200 scale (grids/A): 3.645715 object centre (A): 101.4255 89.27299 58.00100 number of atom coordinates read : 1076 total number of charged atoms : 941 net assigned charge : 0.1340044 assigned positive charge : 150.1141 centred at (gu) : 91.29957 85.18990 87.00017 assigned negative charge : -149.9801 centred at (gu) : 92.03327 84.28730 86.82101 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 114036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10601 grid for indexing accessible points = 1.400000 m= 57389 mr = 77453 m= 25758 mr = 46269 m= 8960 mr = 20987 m= 2498 mr = 7095 m= 516 mr = 1942 m= 79 mr = 403 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 7367 time to turn everything in is 0.8100000 number of dielectric boundary points 55038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 7528 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) : 2.430476 object centre at (A) : 101.4255 89.27299 58.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5746047E-02 0.1476346 midg,1,midg; midg,igrid,midg 0.1183414 0.2406497 1,midg,midg; igrid,midg,midg 0.1360451 -0.1583000 gauss-seidel spectral radius is 0.9993241 estimated iterations to convergence 303 setup time was (sec) 1.050000 now iterating at: 08:41:46 rms-change max change #iterations 8.309613 242.2446 at 10iterations 4.893552 131.3369 at 20iterations 2.885098 65.93671 at 30iterations 1.692883 36.41448 at 40iterations 0.9952418 20.43732 at 50iterations 0.5842148 12.11942 at 60iterations 0.3430805 6.789120 at 70iterations 0.2016588 3.910862 at 80iterations 0.1185406 2.420979 at 90iterations 6.9544949E-02 1.397575 at 100iterations 4.0844012E-02 0.7437210 at 110iterations 2.4055844E-02 0.4816895 at 120iterations 1.4053262E-02 0.3072624 at 130iterations 8.2825553E-03 0.1611290 at 140iterations 4.8657628E-03 9.8976016E-02 at 150iterations 2.8575449E-03 5.4252625E-02 at 160iterations 1.6799269E-03 3.1343460E-02 at 170iterations 9.8584755E-04 1.8920898E-02 at 180iterations finished qdiffx linear iterations at : 08:41:57 total time elapsed so far: 11.90000 # loops : 180 mean,max change (kT/e) : 9.8584755E-04 1.8920898E-02 energy calculations done at 11.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.04000 DelPhi exited at 08:41:58 12.038u 0.216s 0:12.62 96.9% 0+0k 0+0io 0pf+0w