Thu Jan 19 13:34:57 PST 2012 #!/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 Thu Jan 19 2012 at 13:34:59 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6895 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4369438 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): -2.108000 79.36700 ymin,ymax (A): -11.90100 65.41200 zmin,zma (A): -23.57400 43.11500 x,y,z range (A): 81.47501 77.31300 66.68900 scale (grids/A): 0.4369438 object centre (A): 38.62950 26.75550 9.770499 number of atom coordinates read : 6895 total number of charged atoms : 6723 net assigned charge : 0.2000409 assigned positive charge : 1053.985 centred at (gu) : 87.60189 90.27415 89.55527 assigned negative charge : -1053.794 centred at (gu) : 87.52686 90.33852 89.45925 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7658 nv = 96 ne = 84 npr = 141419 no. pairs analyzed = 141419 no. exposed pairs = 8725 no. arc points = 59460 no. surface atoms = 2907 nbur = 3988 mkacc time = 0.2500000 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 = 1.904000 m= 187 mr = 3673 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.4500000 number of dielectric boundary points 4170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4992 ## 1038 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10611 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0332061E-11 8.1839500E-12 midg,1,midg; midg,igrid,midg 5.9074642E-12 -6.4176095E-12 1,midg,midg; igrid,midg,midg -1.4720709E-11 3.5809465E-12 gauss-seidel spectral radius is 0.9734156 estimated iterations to convergence 51 setup time was (sec) 0.6600000 now iterating at: 13:35:00 rms-change max change #iterations 3.4387439E-02 6.202286 at 10iterations 1.6735764E-03 0.2613068 at 20iterations 4.5633479E-04 7.5293779E-02 at 30iterations 1.8755121E-04 3.2295704E-02 at 40iterations 7.9348822E-05 1.3817549E-02 at 50iterations finished qdiffx linear iterations at : 13:35:08 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 7.9348822E-05 1.3817549E-02 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 13:35:09 3.930u 0.185s 0:10.17 40.4% 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 Thu Jan 19 2012 at 13:35:09 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6895 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.310831 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): -2.108000 79.36700 ymin,ymax (A): -11.90100 65.41200 zmin,zma (A): -23.57400 43.11500 x,y,z range (A): 81.47501 77.31300 66.68900 scale (grids/A): 1.310831 object centre (A): 38.62950 26.75550 9.770499 number of atom coordinates read : 6895 total number of charged atoms : 6723 net assigned charge : 0.2000409 assigned positive charge : 1053.985 centred at (gu) : 82.80365 90.82073 88.66372 assigned negative charge : -1053.794 centred at (gu) : 82.58005 91.01541 88.37743 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 89056 reading accessible surface arcs data from file ARCDAT no. of arc points read = 59460 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 19978 mr = 58776 m= 898 mr = 11749 m= 10 mr = 213 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1063 time to turn everything in is 0.4800000 number of dielectric boundary points 39204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1037 ## 29 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 46972 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) : 0.4369438 object centre at (A) : 38.62950 26.75550 9.770499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3739136E-03 2.6061484E-03 midg,1,midg; midg,igrid,midg 6.3258219E-03 1.2372810E-03 1,midg,midg; igrid,midg,midg -1.7825348E-02 1.1218436E-03 gauss-seidel spectral radius is 0.9974992 estimated iterations to convergence 159 setup time was (sec) 0.7200000 now iterating at: 13:35:12 rms-change max change #iterations 3.223934 148.4879 at 10iterations 1.150763 42.84956 at 20iterations 0.4140296 15.09829 at 30iterations 0.1494198 5.346668 at 40iterations 5.3542838E-02 1.951565 at 50iterations 1.9334914E-02 0.7250977 at 60iterations 6.9427220E-03 0.2299252 at 70iterations 2.5405823E-03 8.1741333E-02 at 80iterations 9.4939995E-04 3.2248259E-02 at 90iterations 3.8760435E-04 1.5548706E-02 at 100iterations 1.9014937E-04 7.1964264E-03 at 110iterations 1.1511002E-04 3.8452148E-03 at 120iterations finished qdiffx linear iterations at : 13:35:36 total time elapsed so far: 8.140000 # loops : 120 mean,max change (kT/e) : 1.1511002E-04 3.8452148E-03 energy calculations done at 8.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.280000 DelPhi exited at 13:35:36 8.278u 0.221s 0:27.24 31.1% 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 Thu Jan 19 2012 at 13:35:37 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: 360 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6895 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.966247 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): -2.108000 79.36700 ymin,ymax (A): -11.90100 65.41200 zmin,zma (A): -23.57400 43.11500 x,y,z range (A): 81.47501 77.31300 66.68900 scale (grids/A): 1.966247 object centre (A): 38.62950 26.75550 9.770499 number of atom coordinates read : 6895 total number of charged atoms : 6723 net assigned charge : 0.2000409 assigned positive charge : 1053.985 centred at (gu) : 79.20516 91.23058 87.99516 assigned negative charge : -1053.794 centred at (gu) : 78.87002 91.52292 87.56609 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 209160 reading accessible surface arcs data from file ARCDAT no. of arc points read = 59460 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 78474 mr = 146739 m= 13429 mr = 57780 m= 907 mr = 8509 m= 9 mr = 360 m= 0 mr = 0 time to grow re-entrant surface = 0.5699999 no. cavity mid-points inaccessible to solvent = 3588 time to turn everything in is 1.060000 number of dielectric boundary points 88591 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 296 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 53114 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) : 1.310831 object centre at (A) : 38.62950 26.75550 9.770499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1046733 6.1884034E-02 midg,1,midg; midg,igrid,midg 0.2356082 8.7969087E-02 1,midg,midg; igrid,midg,midg -0.5202210 6.0779091E-02 gauss-seidel spectral radius is 0.9990118 estimated iterations to convergence 252 setup time was (sec) 1.350000 now iterating at: 13:35:39 rms-change max change #iterations 9.784862 312.4779 at 10iterations 5.336277 149.3297 at 20iterations 2.889352 68.88609 at 30iterations 1.558830 34.39521 at 40iterations 0.8351693 18.44169 at 50iterations 0.4464421 9.463112 at 60iterations 0.2381909 5.806976 at 70iterations 0.1267586 2.683719 at 80iterations 6.7285784E-02 1.585392 at 90iterations 3.5657201E-02 0.7033749 at 100iterations 1.8933050E-02 0.3819962 at 110iterations 1.0022744E-02 0.2056656 at 120iterations 5.3226696E-03 0.1142464 at 130iterations 2.8301943E-03 6.4905167E-02 at 140iterations 1.5066940E-03 3.1860352E-02 at 150iterations 8.1246393E-04 1.6989708E-02 at 160iterations 4.4644577E-04 9.6740723E-03 at 170iterations 2.5622261E-04 5.4931641E-03 at 180iterations finished qdiffx linear iterations at : 13:36:05 total time elapsed so far: 13.88000 # loops : 180 mean,max change (kT/e) : 2.5622261E-04 5.4931641E-03 energy calculations done at 13.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.01000 DelPhi exited at 13:36:06 14.015u 0.255s 0:28.98 49.2% 0+0k 0+0io 0pf+0w