Thu Jan 19 13:33:02 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 13:33:02 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: 394 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6695 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: ARG 66 has a net charge of 0.0400 !!! WARNING: ASH 70 has a net charge of -0.3190 !!! WARNING: ARG 126 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: GLN 251 has a net charge of 0.0170 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 422 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: HEM 1107 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4386938 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): 210.3660 275.7610 ymin,ymax (A): 62.71000 139.1200 zmin,zma (A): -67.32000 13.83000 x,y,z range (A): 65.39497 76.41000 81.15000 scale (grids/A): 0.4386938 object centre (A): 243.0635 100.9150 -26.74500 number of atom coordinates read : 6695 total number of charged atoms : 6522 net assigned charge : -7.026945 assigned positive charge : 1007.886 centred at (gu) : 90.89677 90.08731 88.05664 assigned negative charge : -1014.922 centred at (gu) : 90.88881 90.02814 88.05451 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7717 nv = 96 ne = 84 npr = 135052 no. pairs analyzed = 135052 no. exposed pairs = 9036 no. arc points = 59700 no. surface atoms = 3055 nbur = 3640 mkacc time = 0.2300000 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= 218 mr = 3596 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 4339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5047 ## 963 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10573 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7053811E-12 -1.2412625E-12 midg,1,midg; midg,igrid,midg -8.2984340E-12 3.6998755E-12 1,midg,midg; igrid,midg,midg -2.4683669E-12 -2.0668658E-12 gauss-seidel spectral radius is 0.9736215 estimated iterations to convergence 51 setup time was (sec) 0.6600000 now iterating at: 13:33:03 rms-change max change #iterations 3.4066692E-02 5.416169 at 10iterations 2.3060918E-03 0.3402309 at 20iterations 8.8206452E-04 0.1411791 at 30iterations 3.9723358E-04 6.3993454E-02 at 40iterations 1.7934843E-04 2.9048920E-02 at 50iterations finished qdiffx linear iterations at : 13:33:09 total time elapsed so far: 3.740000 # loops : 50 mean,max change (kT/e) : 1.7934843E-04 2.9048920E-02 energy calculations done at 3.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.880000 DelPhi exited at 13:33:09 3.882u 0.215s 0:07.51 54.4% 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 13:33:09 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: 394 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6695 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: ARG 66 has a net charge of 0.0400 !!! WARNING: ASH 70 has a net charge of -0.3190 !!! WARNING: ARG 126 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: GLN 251 has a net charge of 0.0170 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 422 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: HEM 1107 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.316081 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): 210.3660 275.7610 ymin,ymax (A): 62.71000 139.1200 zmin,zma (A): -67.32000 13.83000 x,y,z range (A): 65.39497 76.41000 81.15000 scale (grids/A): 1.316081 object centre (A): 243.0635 100.9150 -26.74500 number of atom coordinates read : 6695 total number of charged atoms : 6522 net assigned charge : -7.026945 assigned positive charge : 1007.886 centred at (gu) : 92.68849 90.25935 84.16835 assigned negative charge : -1014.922 centred at (gu) : 92.66614 90.08426 84.16299 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 88815 reading accessible surface arcs data from file ARCDAT no. of arc points read = 59700 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 21875 mr = 57880 m= 1280 mr = 12880 m= 18 mr = 311 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 40917 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 912 ## 25 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 45742 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) : 0.4386938 object centre at (A) : 243.0635 100.9150 -26.74500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9379614E-03 -1.5953145E-03 midg,1,midg; midg,igrid,midg -7.0468290E-04 9.9845289E-04 1,midg,midg; igrid,midg,midg -1.9128318E-03 -1.2863114E-03 gauss-seidel spectral radius is 0.9975182 estimated iterations to convergence 160 setup time was (sec) 0.7300000 now iterating at: 13:33:10 rms-change max change #iterations 3.209142 127.1099 at 10iterations 1.152996 39.70673 at 20iterations 0.4168096 14.21220 at 30iterations 0.1502803 5.447917 at 40iterations 5.4364704E-02 1.940745 at 50iterations 1.9865070E-02 0.7737126 at 60iterations 7.5134216E-03 0.3073044 at 70iterations 3.1645021E-03 0.1217613 at 80iterations 1.6568645E-03 5.9078217E-02 at 90iterations 1.0687675E-03 3.5869598E-02 at 100iterations 7.6127984E-04 2.4271011E-02 at 110iterations 5.5689045E-04 1.7379761E-02 at 120iterations finished qdiffx linear iterations at : 13:33:25 total time elapsed so far: 8.120000 # loops : 120 mean,max change (kT/e) : 5.5689045E-04 1.7379761E-02 energy calculations done at 8.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.260000 DelPhi exited at 13:33:26 8.263u 0.268s 0:16.59 51.3% 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 13:33:26 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: 394 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6695 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: ARG 66 has a net charge of 0.0400 !!! WARNING: ASH 70 has a net charge of -0.3190 !!! WARNING: ARG 126 has a net charge of 0.0400 !!! WARNING: LYS 137 has a net charge of 0.0200 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: ARG 148 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: GLN 251 has a net charge of 0.0170 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 422 has a net charge of 0.0200 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: LYS 542 has a net charge of 0.0200 !!! WARNING: HEM 1107 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.974122 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): 210.3660 275.7610 ymin,ymax (A): 62.71000 139.1200 zmin,zma (A): -67.32000 13.83000 x,y,z range (A): 65.39497 76.41000 81.15000 scale (grids/A): 1.974122 object centre (A): 243.0635 100.9150 -26.74500 number of atom coordinates read : 6695 total number of charged atoms : 6522 net assigned charge : -7.026945 assigned positive charge : 1007.886 centred at (gu) : 94.03213 90.38860 81.25198 assigned negative charge : -1014.922 centred at (gu) : 93.99899 90.12617 81.24442 start vw surface at 0.1700000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 207771 reading accessible surface arcs data from file ARCDAT no. of arc points read = 59700 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 83372 mr = 144719 m= 16327 mr = 61036 m= 1419 mr = 10167 m= 28 mr = 577 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.130000 number of dielectric boundary points 92418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 250 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 51556 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) : 1.316081 object centre at (A) : 243.0635 100.9150 -26.74500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7068581 1.0070652E-02 midg,1,midg; midg,igrid,midg -5.8006602E-03 3.9904598E-02 1,midg,midg; igrid,midg,midg -7.2140679E-02 -1.4431814E-03 gauss-seidel spectral radius is 0.9990143 estimated iterations to convergence 252 setup time was (sec) 1.440000 now iterating at: 13:33:30 rms-change max change #iterations 9.784300 251.4244 at 10iterations 5.379219 137.0244 at 20iterations 2.928865 75.59511 at 30iterations 1.584019 38.43188 at 40iterations 0.8495108 19.07173 at 50iterations 0.4553953 11.85359 at 60iterations 0.2434037 5.044233 at 70iterations 0.1293513 3.101478 at 80iterations 6.8782188E-02 1.520924 at 90iterations 3.6648098E-02 0.7181730 at 100iterations 1.9397458E-02 0.4257355 at 110iterations 1.0309908E-02 0.2109776 at 120iterations 5.4805740E-03 0.1197758 at 130iterations 2.9241100E-03 5.5261612E-02 at 140iterations 1.5723623E-03 3.1440735E-02 at 150iterations 8.6596439E-04 1.7798424E-02 at 160iterations 4.9619470E-04 1.0471344E-02 at 170iterations 3.0415587E-04 6.5975189E-03 at 180iterations finished qdiffx linear iterations at : 13:33:48 total time elapsed so far: 14.24000 # loops : 180 mean,max change (kT/e) : 3.0415587E-04 6.5975189E-03 energy calculations done at 14.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.37000 DelPhi exited at 13:33:49 14.367u 0.317s 0:22.80 64.3% 0+0k 0+0io 0pf+0w