Tue Oct 11 06:32:17 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+sph.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 = amb.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 06:32:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 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: 0.7076972 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): -40.53500 -0.3960000 ymin,ymax (A): -27.47400 18.78400 zmin,zma (A): -15.07000 35.23400 x,y,z range (A): 40.13900 46.25800 50.30400 scale (grids/A): 0.7076972 object centre (A): -20.46550 -4.344999 10.08200 number of atom coordinates read : 2064 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 91.21306 89.95603 88.71941 assigned negative charge : -311.0742 centred at (gu) : 91.25191 90.07697 88.64612 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6966 nv = 96 ne = 84 npr = 41037 no. pairs analyzed = 41037 no. exposed pairs = 2459 no. arc points = 16976 no. surface atoms = 840 nbur = 1224 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 466 mr = 4006 m= 4 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.3200000 number of dielectric boundary points 3335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1643 ## 154 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7813 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3923716E-08 7.1867738E-08 midg,1,midg; midg,igrid,midg 1.1586451E-07 -4.6032680E-09 1,midg,midg; igrid,midg,midg 5.9556427E-08 4.5633165E-08 gauss-seidel spectral radius is 0.9895896 estimated iterations to convergence 80 setup time was (sec) 0.5500000 now iterating at: 06:32:18 rms-change max change #iterations 0.2064851 29.50985 at 10iterations 2.5426719E-02 3.583763 at 20iterations 3.3219154E-03 0.4456120 at 30iterations 4.8479656E-04 5.7891846E-02 at 40iterations 9.1209375E-05 1.0913849E-02 at 50iterations finished qdiffx linear iterations at : 06:32:21 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 9.1209375E-05 1.0913849E-02 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 06:32:21 3.250u 0.164s 0:04.22 80.8% 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 06:32:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 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: 2.123091 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): -40.53500 -0.3960000 ymin,ymax (A): -27.47400 18.78400 zmin,zma (A): -15.07000 35.23400 x,y,z range (A): 40.13900 46.25800 50.30400 scale (grids/A): 2.123091 object centre (A): -20.46550 -4.344999 10.08200 number of atom coordinates read : 2064 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 93.63902 89.86789 86.15825 assigned negative charge : -311.0742 centred at (gu) : 93.75596 90.23092 85.93843 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16976 grid for indexing accessible points = 1.400000 m= 29969 mr = 52700 m= 6064 mr = 22914 m= 629 mr = 4213 m= 18 mr = 356 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 553 time to turn everything in is 0.5600000 number of dielectric boundary points 30706 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 15557 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) : 0.7076972 object centre at (A) : -20.46550 -4.344999 10.08200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0973429E-02 3.7418742E-02 midg,1,midg; midg,igrid,midg 4.5304634E-02 1.2088089E-02 1,midg,midg; igrid,midg,midg 1.3294639E-02 2.5712341E-02 gauss-seidel spectral radius is 0.9988286 estimated iterations to convergence 231 setup time was (sec) 0.8600000 now iterating at: 06:32:23 rms-change max change #iterations 4.621666 238.5235 at 10iterations 2.291170 88.24843 at 20iterations 1.142019 34.83376 at 30iterations 0.5647561 17.44582 at 40iterations 0.2807276 8.691571 at 50iterations 0.1394792 4.338032 at 60iterations 6.9419168E-02 2.121342 at 70iterations 3.4491066E-02 1.047470 at 80iterations 1.7138850E-02 0.5254288 at 90iterations 8.5642627E-03 0.2615395 at 100iterations 4.2704381E-03 0.1300468 at 110iterations 2.1622411E-03 6.0791016E-02 at 120iterations finished qdiffx linear iterations at : 06:32:29 total time elapsed so far: 7.140000 # loops : 120 mean,max change (kT/e) : 2.1622411E-03 6.0791016E-02 energy calculations done at 7.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.310000 DelPhi exited at 06:32:29 7.317u 0.212s 0:07.92 94.9% 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 06:32:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2064 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: 3.184637 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): -40.53500 -0.3960000 ymin,ymax (A): -27.47400 18.78400 zmin,zma (A): -15.07000 35.23400 x,y,z range (A): 40.13900 46.25800 50.30400 scale (grids/A): 3.184637 object centre (A): -20.46550 -4.344999 10.08200 number of atom coordinates read : 2064 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 95.45847 89.80195 84.23735 assigned negative charge : -311.0742 centred at (gu) : 95.63393 90.34634 83.90762 start vw surface at 0.1700000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 170930 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16976 grid for indexing accessible points = 1.400000 m= 92927 mr = 126684 m= 38428 mr = 77609 m= 11562 mr = 31922 m= 2616 mr = 9188 m= 363 mr = 2011 m= 21 mr = 276 m= 0 mr = 3 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 1913 time to turn everything in is 1.720000 number of dielectric boundary points 69154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 15688 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) : 2.123091 object centre at (A) : -20.46550 -4.344999 10.08200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3411557 0.1976957 midg,1,midg; midg,igrid,midg 0.3597142 8.7237827E-02 1,midg,midg; igrid,midg,midg 7.7872284E-02 0.2577810 gauss-seidel spectral radius is 0.9992969 estimated iterations to convergence 298 setup time was (sec) 2.000000 now iterating at: 06:32:32 rms-change max change #iterations 10.26269 413.2791 at 10iterations 6.061863 201.2575 at 20iterations 3.579932 89.29575 at 30iterations 2.112695 38.95996 at 40iterations 1.240461 25.13304 at 50iterations 0.7304968 13.09073 at 60iterations 0.4280336 8.010417 at 70iterations 0.2508579 4.581793 at 80iterations 0.1469922 2.528114 at 90iterations 8.6189322E-02 1.536358 at 100iterations 5.0611716E-02 0.9281235 at 110iterations 2.9798659E-02 0.5300789 at 120iterations 1.7628519E-02 0.3274956 at 130iterations 1.0537167E-02 0.1836929 at 140iterations 6.4132083E-03 0.1226425 at 150iterations 4.0071821E-03 7.4813843E-02 at 160iterations 2.6169580E-03 4.8019409E-02 at 170iterations 1.7968054E-03 3.4315109E-02 at 180iterations finished qdiffx linear iterations at : 06:32:42 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 1.7968054E-03 3.4315109E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.58000 DelPhi exited at 06:32:43 12.586u 0.200s 0:13.26 96.3% 0+0k 0+0io 0pf+0w