Tue Oct 11 07:37:06 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 Tue Oct 11 2011 at 07:37:06 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3149 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: 0.6164609 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): 71.28800 122.6200 ymin,ymax (A): -15.85500 36.30000 zmin,zma (A): -26.49100 31.25800 x,y,z range (A): 51.33200 52.15500 57.74900 scale (grids/A): 0.6164609 object centre (A): 96.95400 10.22250 2.383499 number of atom coordinates read : 3149 total number of charged atoms : 3001 net assigned charge : 8.8512897E-06 assigned positive charge : 472.0809 centred at (gu) : 89.82905 90.22620 90.69825 assigned negative charge : -472.0820 centred at (gu) : 89.95258 90.17094 90.65018 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7793 nv = 96 ne = 84 npr = 66142 no. pairs analyzed = 66142 no. exposed pairs = 3593 no. arc points = 24559 no. surface atoms = 1236 nbur = 1913 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 355 mr = 4536 m= 0 mr = 37 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.4100000 number of dielectric boundary points 3575 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2482 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9755 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0531573E-09 4.0293573E-09 midg,1,midg; midg,igrid,midg -3.8985264E-09 4.1652397E-09 1,midg,midg; igrid,midg,midg 9.1861168E-09 -8.8367074E-09 gauss-seidel spectral radius is 0.9864127 estimated iterations to convergence 70 setup time was (sec) 0.6700000 now iterating at: 07:37:07 rms-change max change #iterations 0.1401809 20.73143 at 10iterations 1.3025013E-02 1.743534 at 20iterations 1.3833714E-03 0.1868134 at 30iterations 2.3382575E-04 3.8784027E-02 at 40iterations 5.5980385E-05 9.9906921E-03 at 50iterations finished qdiffx linear iterations at : 07:37:10 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 5.5980385E-05 9.9906921E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 07:37:11 4.120u 0.261s 0:04.68 93.5% 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 07:37:11 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3149 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.849383 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): 71.28800 122.6200 ymin,ymax (A): -15.85500 36.30000 zmin,zma (A): -26.49100 31.25800 x,y,z range (A): 51.33200 52.15500 57.74900 scale (grids/A): 1.849383 object centre (A): 96.95400 10.22250 2.383499 number of atom coordinates read : 3149 total number of charged atoms : 3001 net assigned charge : 8.8512897E-06 assigned positive charge : 472.0809 centred at (gu) : 89.48620 90.67766 92.09373 assigned negative charge : -472.0820 centred at (gu) : 89.85749 90.51224 91.94981 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 85592 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24559 grid for indexing accessible points = 1.400000 m= 30021 mr = 61789 m= 4000 mr = 22507 m= 162 mr = 2413 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 3047 time to turn everything in is 0.7400000 number of dielectric boundary points 33011 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 199 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 23511 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) : 0.6164609 object centre at (A) : 96.95400 10.22250 2.383499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5076750E-03 5.2595125E-03 midg,1,midg; midg,igrid,midg -2.0014450E-02 -9.5616942E-03 1,midg,midg; igrid,midg,midg 2.4120465E-02 -1.6798137E-02 gauss-seidel spectral radius is 0.9986007 estimated iterations to convergence 212 setup time was (sec) 1.040000 now iterating at: 07:37:12 rms-change max change #iterations 4.481975 168.9671 at 10iterations 2.072712 67.95186 at 20iterations 0.9635431 30.64898 at 30iterations 0.4484996 13.90538 at 40iterations 0.2086781 6.990349 at 50iterations 9.7147763E-02 3.015297 at 60iterations 4.5332436E-02 1.378781 at 70iterations 2.1067822E-02 0.6511784 at 80iterations 9.8333741E-03 0.3015442 at 90iterations 4.5967610E-03 0.1356770 at 100iterations 2.1543778E-03 6.6709518E-02 at 110iterations 1.0116362E-03 3.0330658E-02 at 120iterations finished qdiffx linear iterations at : 07:37:20 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 1.0116362E-03 3.0330658E-02 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.520000 DelPhi exited at 07:37:21 9.527u 0.291s 0:10.10 97.1% 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 07:37:21 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3149 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: 2.774074 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): 71.28800 122.6200 ymin,ymax (A): -15.85500 36.30000 zmin,zma (A): -26.49100 31.25800 x,y,z range (A): 51.33200 52.15500 57.74900 scale (grids/A): 2.774074 object centre (A): 96.95400 10.22250 2.383499 number of atom coordinates read : 3149 total number of charged atoms : 3001 net assigned charge : 8.8512897E-06 assigned positive charge : 472.0809 centred at (gu) : 89.22906 91.01630 93.14043 assigned negative charge : -472.0820 centred at (gu) : 89.78613 90.76829 92.92465 start vw surface at 0.1900000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 198457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24559 grid for indexing accessible points = 1.400000 m= 99639 mr = 149261 m= 33206 mr = 82990 m= 6878 mr = 26700 m= 754 mr = 5223 m= 27 mr = 486 m= 0 mr = 7 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 10162 time to turn everything in is 1.910000 number of dielectric boundary points 74294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 24006 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) : 1.849383 object centre at (A) : 96.95400 10.22250 2.383499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3723445E-02 -8.6160660E-02 midg,1,midg; midg,igrid,midg -0.2303225 -0.2087712 1,midg,midg; igrid,midg,midg 0.2463082 -0.2243068 gauss-seidel spectral radius is 0.9992521 estimated iterations to convergence 289 setup time was (sec) 2.230000 now iterating at: 07:37:23 rms-change max change #iterations 10.56661 309.8494 at 10iterations 6.158017 123.9612 at 20iterations 3.560331 80.15403 at 30iterations 2.057243 37.29758 at 40iterations 1.185204 24.41636 at 50iterations 0.6824145 12.42049 at 60iterations 0.3922001 7.297115 at 70iterations 0.2254413 4.516231 at 80iterations 0.1294626 2.295980 at 90iterations 7.4325159E-02 1.425244 at 100iterations 4.2740803E-02 0.7404311 at 110iterations 2.4481386E-02 0.4076529 at 120iterations 1.4085786E-02 0.2493782 at 130iterations 8.0913734E-03 0.1414638 at 140iterations 4.6798796E-03 7.5902939E-02 at 150iterations 2.7247730E-03 4.9802780E-02 at 160iterations 1.5948133E-03 2.7712822E-02 at 170iterations 9.5032289E-04 1.7416000E-02 at 180iterations finished qdiffx linear iterations at : 07:37:37 total time elapsed so far: 15.99000 # loops : 180 mean,max change (kT/e) : 9.5032289E-04 1.7416000E-02 energy calculations done at 15.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.16000 DelPhi exited at 07:37:38 16.166u 0.298s 0:16.88 97.4% 0+0k 0+0io 0pf+0w