Sat Oct 15 10:47:06 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 15 2011 at 10:47:06 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 = 4298 !!! WARNING: HIQ 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5835778 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): -25.09700 35.90600 ymin,ymax (A): 37.81500 97.67800 zmin,zma (A): 29.24800 88.22200 x,y,z range (A): 61.00300 59.86300 58.97400 scale (grids/A): 0.5835778 object centre (A): 5.404501 67.74651 58.73500 number of atom coordinates read : 4298 total number of charged atoms : 4163 net assigned charge : -5.485941 assigned positive charge : 647.3645 centred at (gu) : 90.65918 88.47209 88.91016 assigned negative charge : -652.8534 centred at (gu) : 90.50587 88.58741 89.03807 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 9445 nv = 96 ne = 84 npr = 90229 no. pairs analyzed = 90229 no. exposed pairs = 4802 no. arc points = 32699 no. surface atoms = 1630 nbur = 2668 mkacc time = 0.2000000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 438 mr = 5603 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.4200000 number of dielectric boundary points 4227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3413 ## 382 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 12355 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9883821E-09 -4.8241597E-09 midg,1,midg; midg,igrid,midg 3.8029597E-09 -4.0316452E-09 1,midg,midg; igrid,midg,midg -6.1462480E-09 4.6314508E-09 gauss-seidel spectral radius is 0.9849365 estimated iterations to convergence 67 setup time was (sec) 0.6500000 now iterating at: 10:47:07 rms-change max change #iterations 0.1258294 18.68402 at 10iterations 1.0494741E-02 1.429898 at 20iterations 1.1701512E-03 0.1407623 at 30iterations 2.7372560E-04 3.3958197E-02 at 40iterations 9.1749505E-05 1.1974812E-02 at 50iterations finished qdiffx linear iterations at : 10:47:10 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 9.1749505E-05 1.1974812E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 10:47:10 3.471u 0.201s 0:03.96 92.6% 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 15 2011 at 10:47:10 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 = 4298 !!! WARNING: HIQ 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.750733 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): -25.09700 35.90600 ymin,ymax (A): 37.81500 97.67800 zmin,zma (A): 29.24800 88.22200 x,y,z range (A): 61.00300 59.86300 58.97400 scale (grids/A): 1.750733 object centre (A): 5.404501 67.74651 58.73500 number of atom coordinates read : 4298 total number of charged atoms : 4163 net assigned charge : -5.485941 assigned positive charge : 647.3645 centred at (gu) : 91.97659 85.41523 86.72931 assigned negative charge : -652.8534 centred at (gu) : 91.51723 85.76180 87.11349 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 105411 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32699 grid for indexing accessible points = 1.400000 m= 36494 mr = 77349 m= 4800 mr = 27132 m= 165 mr = 2984 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 4168 time to turn everything in is 0.7100000 number of dielectric boundary points 39367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 306 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 32423 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) : 0.5835778 object centre at (A) : 5.404501 67.74651 58.73500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3128870E-02 -3.1773884E-02 midg,1,midg; midg,igrid,midg 2.8477389E-02 -7.2249048E-03 1,midg,midg; igrid,midg,midg -2.1800030E-02 3.7977025E-02 gauss-seidel spectral radius is 0.9985383 estimated iterations to convergence 207 setup time was (sec) 1.020000 now iterating at: 10:47:12 rms-change max change #iterations 4.793594 163.3129 at 10iterations 2.187357 58.86746 at 20iterations 0.9981616 30.09149 at 30iterations 0.4568672 13.27622 at 40iterations 0.2092473 5.820166 at 50iterations 9.5395595E-02 2.846012 at 60iterations 4.3802660E-02 1.227663 at 70iterations 2.0062122E-02 0.5401173 at 80iterations 9.1941515E-03 0.2677612 at 90iterations 4.2570131E-03 0.1150007 at 100iterations 1.9837418E-03 5.3839684E-02 at 110iterations 9.4343483E-04 2.8717041E-02 at 120iterations finished qdiffx linear iterations at : 10:47:18 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 9.4343483E-04 2.8717041E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 10:47:19 8.030u 0.202s 0:08.75 94.0% 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 Sat Oct 15 2011 at 10:47:19 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 = 4298 !!! WARNING: HIQ 440 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.626100 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): -25.09700 35.90600 ymin,ymax (A): 37.81500 97.67800 zmin,zma (A): 29.24800 88.22200 x,y,z range (A): 61.00300 59.86300 58.97400 scale (grids/A): 2.626100 object centre (A): 5.404501 67.74651 58.73500 number of atom coordinates read : 4298 total number of charged atoms : 4163 net assigned charge : -5.485941 assigned positive charge : 647.3645 centred at (gu) : 92.96444 83.12241 85.09361 assigned negative charge : -652.8534 centred at (gu) : 92.27581 83.64267 85.67007 start vw surface at 0.1900000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 245007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32699 grid for indexing accessible points = 1.400000 m= 122934 mr = 187397 m= 39742 mr = 102143 m= 8266 mr = 31845 m= 850 mr = 6259 m= 26 mr = 508 m= 0 mr = 6 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 13834 time to turn everything in is 1.820000 number of dielectric boundary points 88667 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 33289 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) : 1.750733 object centre at (A) : 5.404501 67.74651 58.73500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1571642 -0.3811055 midg,1,midg; midg,igrid,midg 0.4666808 -2.3539728E-02 1,midg,midg; igrid,midg,midg -0.1512546 0.5220492 gauss-seidel spectral radius is 0.9992581 estimated iterations to convergence 290 setup time was (sec) 2.130000 now iterating at: 10:47:21 rms-change max change #iterations 11.64343 270.1282 at 10iterations 6.804132 129.7086 at 20iterations 3.941300 67.98299 at 30iterations 2.283612 41.41475 at 40iterations 1.322885 22.20507 at 50iterations 0.7618420 12.46504 at 60iterations 0.4392129 7.026052 at 70iterations 0.2530178 4.050026 at 80iterations 0.1458521 2.328304 at 90iterations 8.3783276E-02 1.593319 at 100iterations 4.8250824E-02 0.7082703 at 110iterations 2.7820490E-02 0.4636955 at 120iterations 1.6011376E-02 0.2475739 at 130iterations 9.2444327E-03 0.1396103 at 140iterations 5.3539518E-03 8.5990906E-02 at 150iterations 3.1084171E-03 4.9694061E-02 at 160iterations 1.8317705E-03 3.3653259E-02 at 170iterations 1.0967857E-03 1.7791748E-02 at 180iterations finished qdiffx linear iterations at : 10:47:33 total time elapsed so far: 13.26000 # loops : 180 mean,max change (kT/e) : 1.0967857E-03 1.7791748E-02 energy calculations done at 13.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.44000 DelPhi exited at 10:47:33 13.437u 0.250s 0:14.04 97.4% 0+0k 0+0io 0pf+0w