Tue Oct 11 03:22:15 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 03:22:15 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 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: 0.5487983 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): -6.485000 45.45300 ymin,ymax (A): -47.87000 16.99900 zmin,zma (A): -20.14900 34.45500 x,y,z range (A): 51.93800 64.86900 54.60400 scale (grids/A): 0.5487983 object centre (A): 19.48400 -15.43550 7.153001 number of atom coordinates read : 3036 total number of charged atoms : 2896 net assigned charge : 4.500034 assigned positive charge : 451.6370 centred at (gu) : 89.44142 90.55386 89.40554 assigned negative charge : -447.1384 centred at (gu) : 89.45203 90.53809 89.39083 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6023 nv = 96 ne = 84 npr = 59807 no. pairs analyzed = 59807 no. exposed pairs = 4320 no. arc points = 30464 no. surface atoms = 1419 nbur = 1617 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 = 1.540000 m= 262 mr = 2848 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2975 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7808 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3277814E-10 3.6474537E-10 midg,1,midg; midg,igrid,midg 1.7133599E-10 4.9052795E-10 1,midg,midg; igrid,midg,midg 4.4718917E-10 2.0454494E-10 gauss-seidel spectral radius is 0.9828959 estimated iterations to convergence 63 setup time was (sec) 0.4000000 now iterating at: 03:22:15 rms-change max change #iterations 7.4512117E-02 12.53307 at 10iterations 5.4110191E-03 0.8636131 at 20iterations 5.2460533E-04 8.6162090E-02 at 30iterations 8.9350746E-05 1.6281128E-02 at 40iterations 1.9333480E-05 3.5610199E-03 at 50iterations finished qdiffx linear iterations at : 03:22:18 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 1.9333480E-05 3.5610199E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 03:22:19 3.387u 0.168s 0:03.88 91.2% 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 03:22:19 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 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: 1.646395 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): -6.485000 45.45300 ymin,ymax (A): -47.87000 16.99900 zmin,zma (A): -20.14900 34.45500 x,y,z range (A): 51.93800 64.86900 54.60400 scale (grids/A): 1.646395 object centre (A): 19.48400 -15.43550 7.153001 number of atom coordinates read : 3036 total number of charged atoms : 2896 net assigned charge : 4.500034 assigned positive charge : 451.6370 centred at (gu) : 88.32339 91.66106 88.21585 assigned negative charge : -447.1384 centred at (gu) : 88.35583 91.61401 88.17212 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65726 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30464 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20472 mr = 42117 m= 2482 mr = 13460 m= 72 mr = 1273 m= 0 mr = 8 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 31894 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 303 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 22292 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) : 0.5487983 object centre at (A) : 19.48400 -15.43550 7.153001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.4183245E-03 3.4143019E-03 midg,1,midg; midg,igrid,midg 5.0617480E-03 5.4691471E-03 1,midg,midg; igrid,midg,midg 3.8597586E-03 7.9596434E-03 gauss-seidel spectral radius is 0.9982466 estimated iterations to convergence 190 setup time was (sec) 0.5500000 now iterating at: 03:22:19 rms-change max change #iterations 3.393064 134.4053 at 10iterations 1.424881 54.78917 at 20iterations 0.6008111 24.57247 at 30iterations 0.2539752 9.094137 at 40iterations 0.1070739 4.508488 at 50iterations 4.5198608E-02 1.543436 at 60iterations 1.9226639E-02 0.6531658 at 70iterations 8.1273150E-03 0.2782898 at 80iterations 3.4506351E-03 0.1209335 at 90iterations 1.4611313E-03 5.9183836E-02 at 100iterations 6.2655978E-04 2.4912834E-02 at 110iterations 2.6815085E-04 9.3493462E-03 at 120iterations finished qdiffx linear iterations at : 03:22:27 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.6815085E-04 9.3493462E-03 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 03:22:27 7.857u 0.204s 0:08.48 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 03:22:27 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3036 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: 2.469592 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): -6.485000 45.45300 ymin,ymax (A): -47.87000 16.99900 zmin,zma (A): -20.14900 34.45500 x,y,z range (A): 51.93800 64.86900 54.60400 scale (grids/A): 2.469592 object centre (A): 19.48400 -15.43550 7.153001 number of atom coordinates read : 3036 total number of charged atoms : 2896 net assigned charge : 4.500034 assigned positive charge : 451.6370 centred at (gu) : 87.48486 92.49149 87.32361 assigned negative charge : -447.1384 centred at (gu) : 87.53362 92.42082 87.25809 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 152586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30464 grid for indexing accessible points = 1.400000 m= 69142 mr = 103933 m= 21304 mr = 52929 m= 3957 mr = 15590 m= 334 mr = 2663 m= 4 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 72034 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 23143 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) : 1.646395 object centre at (A) : 19.48400 -15.43550 7.153001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1774873 2.1130053E-02 midg,1,midg; midg,igrid,midg 8.7506130E-02 4.4819303E-02 1,midg,midg; igrid,midg,midg 8.9634143E-02 0.1860914 gauss-seidel spectral radius is 0.9991694 estimated iterations to convergence 274 setup time was (sec) 1.060000 now iterating at: 03:22:28 rms-change max change #iterations 8.885269 253.2866 at 10iterations 5.109958 135.9868 at 20iterations 2.897612 65.72090 at 30iterations 1.643519 39.13787 at 40iterations 0.9248404 19.75998 at 50iterations 0.5205742 11.92476 at 60iterations 0.2922547 6.033556 at 70iterations 0.1636757 3.574669 at 80iterations 9.1312304E-02 1.840932 at 90iterations 5.1003516E-02 1.109829 at 100iterations 2.8386641E-02 0.5653706 at 110iterations 1.5840912E-02 0.3444843 at 120iterations 8.8281399E-03 0.2005997 at 130iterations 4.9153990E-03 9.8674774E-02 at 140iterations 2.7378146E-03 5.7846069E-02 at 150iterations 1.5272317E-03 3.1324387E-02 at 160iterations 8.5033552E-04 1.8033981E-02 at 170iterations 4.7436016E-04 9.8001957E-03 at 180iterations finished qdiffx linear iterations at : 03:22:40 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 4.7436016E-04 9.8001957E-03 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 03:22:40 12.547u 0.206s 0:13.26 96.0% 0+0k 0+0io 0pf+0w