Sat Oct 15 13:12:48 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 Sat Oct 15 2011 at 13:12:49 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: 368 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2655 !!! WARNING: HIR 108 has a net charge of 0.5140 !!! WARNING: GAR 801 has a net charge of -0.5490 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: 0.5558504 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): -48.99700 15.04900 ymin,ymax (A): 44.03200 95.61700 zmin,zma (A): -33.88800 24.10000 x,y,z range (A): 64.04601 51.58501 57.98800 scale (grids/A): 0.5558504 object centre (A): -16.97400 69.82450 -4.893998 number of atom coordinates read : 2655 total number of charged atoms : 2516 net assigned charge : 0.4650093 assigned positive charge : 417.4267 centred at (gu) : 89.20464 90.33570 91.99827 assigned negative charge : -416.9623 centred at (gu) : 89.19932 90.46058 92.09927 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5429 nv = 96 ne = 84 npr = 51723 no. pairs analyzed = 51723 no. exposed pairs = 3559 no. arc points = 24822 no. surface atoms = 1211 nbur = 1444 mkacc time = 0.1100000 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 = 1.512000 m= 209 mr = 2639 m= 0 mr = 8 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2534 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6952 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8700339E-10 -1.3925848E-09 midg,1,midg; midg,igrid,midg 1.0703033E-09 -1.1532594E-09 1,midg,midg; igrid,midg,midg 2.4763325E-11 9.5268030E-11 gauss-seidel spectral radius is 0.9832875 estimated iterations to convergence 64 setup time was (sec) 0.4900000 now iterating at: 13:12:49 rms-change max change #iterations 8.0771945E-02 13.05439 at 10iterations 5.5699269E-03 1.210037 at 20iterations 4.0983903E-04 8.4852219E-02 at 30iterations 5.1273899E-05 1.3002396E-02 at 40iterations 1.4145395E-05 3.7469864E-03 at 50iterations finished qdiffx linear iterations at : 13:12:52 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.4145395E-05 3.7469864E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 13:12:52 3.115u 0.146s 0:03.72 87.3% 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 15 2011 at 13:12:52 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: 368 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2655 !!! WARNING: HIR 108 has a net charge of 0.5140 !!! WARNING: GAR 801 has a net charge of -0.5490 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: 1.667551 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): -48.99700 15.04900 ymin,ymax (A): 44.03200 95.61700 zmin,zma (A): -33.88800 24.10000 x,y,z range (A): 64.04601 51.58501 57.98800 scale (grids/A): 1.667551 object centre (A): -16.97400 69.82450 -4.893998 number of atom coordinates read : 2655 total number of charged atoms : 2516 net assigned charge : 0.4650093 assigned positive charge : 417.4267 centred at (gu) : 87.61311 91.00665 95.99413 assigned negative charge : -416.9623 centred at (gu) : 87.59774 91.38152 96.29755 start vw surface at 0.1500000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 60210 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24822 grid for indexing accessible points = 1.400000 m= 16859 mr = 39480 m= 1505 mr = 10811 m= 48 mr = 624 m= 0 mr = 6 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 662 time to turn everything in is 0.4400000 number of dielectric boundary points 27701 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 240 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 19356 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) : 0.5558504 object centre at (A) : -16.97400 69.82450 -4.893998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8458363E-03 -2.4652164E-03 midg,1,midg; midg,igrid,midg 9.2468485E-03 -9.9904472E-03 1,midg,midg; igrid,midg,midg -1.0424888E-02 -3.1270429E-03 gauss-seidel spectral radius is 0.9982247 estimated iterations to convergence 188 setup time was (sec) 0.7000000 now iterating at: 13:12:53 rms-change max change #iterations 3.384316 165.6527 at 10iterations 1.409449 55.19215 at 20iterations 0.5927417 22.58195 at 30iterations 0.2488875 10.05094 at 40iterations 0.1041626 4.052258 at 50iterations 4.3915533E-02 1.878329 at 60iterations 1.8438637E-02 0.7307415 at 70iterations 7.7519892E-03 0.2936630 at 80iterations 3.2587696E-03 0.1208855 at 90iterations 1.3710698E-03 5.1992416E-02 at 100iterations 5.8181566E-04 2.1356583E-02 at 110iterations 2.4862628E-04 9.3939304E-03 at 120iterations finished qdiffx linear iterations at : 13:12:59 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 2.4862628E-04 9.3939304E-03 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.880000 DelPhi exited at 13:13:00 6.884u 0.170s 0:07.35 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 Sat Oct 15 2011 at 13:13:00 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: 368 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2655 !!! WARNING: HIR 108 has a net charge of 0.5140 !!! WARNING: GAR 801 has a net charge of -0.5490 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.501327 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): -48.99700 15.04900 ymin,ymax (A): 44.03200 95.61700 zmin,zma (A): -33.88800 24.10000 x,y,z range (A): 64.04601 51.58501 57.98800 scale (grids/A): 2.501327 object centre (A): -16.97400 69.82450 -4.893998 number of atom coordinates read : 2655 total number of charged atoms : 2516 net assigned charge : 0.4650093 assigned positive charge : 417.4267 centred at (gu) : 86.41947 91.50969 98.99103 assigned negative charge : -416.9623 centred at (gu) : 86.39645 92.07217 99.44640 start vw surface at 0.1500000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 139805 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24822 grid for indexing accessible points = 1.400000 m= 60702 mr = 96979 m= 15047 mr = 46701 m= 2173 mr = 10438 m= 153 mr = 1292 m= 4 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 2148 time to turn everything in is 0.9800000 number of dielectric boundary points 62422 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 20113 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) : 1.667551 object centre at (A) : -16.97400 69.82450 -4.893998 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5995545E-02 1.9798629E-02 midg,1,midg; midg,igrid,midg 0.1253529 -0.1298919 1,midg,midg; igrid,midg,midg -0.3921755 -2.7113253E-02 gauss-seidel spectral radius is 0.9991389 estimated iterations to convergence 269 setup time was (sec) 1.260000 now iterating at: 13:13:01 rms-change max change #iterations 8.670361 357.3616 at 10iterations 4.858006 119.9858 at 20iterations 2.722286 71.55396 at 30iterations 1.508984 36.91893 at 40iterations 0.8377183 21.16134 at 50iterations 0.4614522 11.32084 at 60iterations 0.2547988 6.176935 at 70iterations 0.1405730 3.209198 at 80iterations 7.7238485E-02 1.741556 at 90iterations 4.2613667E-02 1.009815 at 100iterations 2.3390699E-02 0.5193119 at 110iterations 1.2866009E-02 0.2782370 at 120iterations 7.0729982E-03 0.1645083 at 130iterations 3.9012192E-03 9.8766327E-02 at 140iterations 2.1463232E-03 5.2615523E-02 at 150iterations 1.1926561E-03 2.7927876E-02 at 160iterations 6.6554238E-04 1.6881943E-02 at 170iterations 3.7780270E-04 1.0023117E-02 at 180iterations finished qdiffx linear iterations at : 13:13:11 total time elapsed so far: 11.14000 # loops : 180 mean,max change (kT/e) : 3.7780270E-04 1.0023117E-02 energy calculations done at 11.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.31000 DelPhi exited at 13:13:12 11.317u 0.182s 0:12.18 94.3% 0+0k 0+0io 0pf+0w