Mon Oct 10 14:24:10 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 Mon Oct 10 2011 at 14:24:10 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6310266 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): -7.986000 44.16000 ymin,ymax (A): 4.247000 60.66300 zmin,zma (A): -14.44900 36.75400 x,y,z range (A): 52.14600 56.41600 51.20300 scale (grids/A): 0.6310266 object centre (A): 18.08700 32.45500 11.15250 number of atom coordinates read : 2400 total number of charged atoms : 2241 net assigned charge : -3.999987 assigned positive charge : 354.0482 centred at (gu) : 90.01505 89.35518 89.98269 assigned negative charge : -358.0485 centred at (gu) : 89.76892 89.41146 90.00084 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6526 nv = 96 ne = 84 npr = 48342 no. pairs analyzed = 48342 no. exposed pairs = 3208 no. arc points = 22753 no. surface atoms = 1081 nbur = 1319 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3341 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2219 ## 195 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7748 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9814482E-09 -5.9984706E-09 midg,1,midg; midg,igrid,midg 2.7730937E-10 -8.0551663E-09 1,midg,midg; igrid,midg,midg -2.5658316E-08 1.5684915E-08 gauss-seidel spectral radius is 0.9869815 estimated iterations to convergence 72 setup time was (sec) 0.3800000 now iterating at: 14:24:11 rms-change max change #iterations 0.1335428 26.72041 at 10iterations 1.2693454E-02 1.918977 at 20iterations 1.2115949E-03 0.1869487 at 30iterations 1.1426944E-04 1.6681671E-02 at 40iterations 1.1255186E-05 1.7127991E-03 at 50iterations finished qdiffx linear iterations at : 14:24:14 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.1255186E-05 1.7127991E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:24:14 3.387u 0.187s 0:03.97 89.6% 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 Mon Oct 10 2011 at 14:24:14 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.893080 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): -7.986000 44.16000 ymin,ymax (A): 4.247000 60.66300 zmin,zma (A): -14.44900 36.75400 x,y,z range (A): 52.14600 56.41600 51.20300 scale (grids/A): 1.893080 object centre (A): 18.08700 32.45500 11.15250 number of atom coordinates read : 2400 total number of charged atoms : 2241 net assigned charge : -3.999987 assigned positive charge : 354.0482 centred at (gu) : 90.04477 88.06522 89.94797 assigned negative charge : -358.0485 centred at (gu) : 89.30672 88.23396 90.00215 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70140 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22753 grid for indexing accessible points = 1.400000 m= 24184 mr = 46925 m= 3521 mr = 17083 m= 203 mr = 1919 m= 6 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3500000 number of dielectric boundary points 32058 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 17640 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) : 0.6310266 object centre at (A) : 18.08700 32.45500 11.15250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6780906E-03 -2.0201853E-02 midg,1,midg; midg,igrid,midg 6.7221681E-03 -9.7534508E-03 1,midg,midg; igrid,midg,midg -4.6051372E-02 1.5664924E-02 gauss-seidel spectral radius is 0.9986068 estimated iterations to convergence 212 setup time was (sec) 0.5600000 now iterating at: 14:24:15 rms-change max change #iterations 3.988353 161.9457 at 10iterations 1.849403 74.75345 at 20iterations 0.8550662 28.07025 at 30iterations 0.3970031 15.69678 at 40iterations 0.1839367 5.589560 at 50iterations 8.5482366E-02 3.025208 at 60iterations 3.9702345E-02 1.305542 at 70iterations 1.8403502E-02 0.5965042 at 80iterations 8.5350247E-03 0.2902832 at 90iterations 3.9666514E-03 0.1416836 at 100iterations 1.8414108E-03 5.9463501E-02 at 110iterations 8.5483288E-04 2.6951313E-02 at 120iterations finished qdiffx linear iterations at : 14:24:22 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 8.5483288E-04 2.6951313E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 14:24:23 7.790u 0.213s 0:08.36 95.6% 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 Mon Oct 10 2011 at 14:24:23 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.839620 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): -7.986000 44.16000 ymin,ymax (A): 4.247000 60.66300 zmin,zma (A): -14.44900 36.75400 x,y,z range (A): 52.14600 56.41600 51.20300 scale (grids/A): 2.839620 object centre (A): 18.08700 32.45500 11.15250 number of atom coordinates read : 2400 total number of charged atoms : 2241 net assigned charge : -3.999987 assigned positive charge : 354.0482 centred at (gu) : 90.06700 87.09778 89.92162 assigned negative charge : -358.0485 centred at (gu) : 88.96000 87.35092 90.00310 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 161812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22753 grid for indexing accessible points = 1.400000 m= 79156 mr = 113886 m= 27149 mr = 63360 m= 6015 mr = 20923 m= 840 mr = 4039 m= 67 mr = 525 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.9000000 number of dielectric boundary points 72275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 17927 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) : 1.893080 object centre at (A) : 18.08700 32.45500 11.15250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9854270E-02 -0.3041985 midg,1,midg; midg,igrid,midg 4.4373699E-02 -8.4012896E-02 1,midg,midg; igrid,midg,midg -0.4589939 9.2648573E-02 gauss-seidel spectral radius is 0.9992565 estimated iterations to convergence 289 setup time was (sec) 1.140000 now iterating at: 14:24:24 rms-change max change #iterations 9.628848 495.2330 at 10iterations 5.681878 140.2484 at 20iterations 3.310316 72.95314 at 30iterations 1.930085 49.19166 at 40iterations 1.116526 23.76691 at 50iterations 0.6471887 15.41846 at 60iterations 0.3742515 7.523205 at 70iterations 0.2153230 4.505083 at 80iterations 0.1238784 2.349554 at 90iterations 7.1435407E-02 1.340248 at 100iterations 4.1026644E-02 0.8406696 at 110iterations 2.3538455E-02 0.4417877 at 120iterations 1.3520637E-02 0.2779160 at 130iterations 7.7533759E-03 0.1500702 at 140iterations 4.4651497E-03 8.5808754E-02 at 150iterations 2.5646319E-03 4.7626495E-02 at 160iterations 1.4698255E-03 2.8530121E-02 at 170iterations 8.4287924E-04 1.6996384E-02 at 180iterations finished qdiffx linear iterations at : 14:24:35 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 8.4287924E-04 1.6996384E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.59000 DelPhi exited at 14:24:36 12.597u 0.205s 0:13.27 96.3% 0+0k 0+0io 0pf+0w