Sat Oct 15 13:30:37 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 Sat Oct 15 2011 at 13:30:37 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: 234 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1998 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5958059 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): -24.91000 34.84100 ymin,ymax (A): -18.50200 20.24600 zmin,zma (A): -4.089000 38.84700 x,y,z range (A): 59.75100 38.74800 42.93600 scale (grids/A): 0.5958059 object centre (A): 4.965502 0.8720007 17.37900 number of atom coordinates read : 1998 total number of charged atoms : 1846 net assigned charge : 3.000005 assigned positive charge : 291.2149 centred at (gu) : 90.00169 90.13805 90.44944 assigned negative charge : -288.2153 centred at (gu) : 90.01099 90.23962 90.58794 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4689 nv = 96 ne = 84 npr = 41502 no. pairs analyzed = 41502 no. exposed pairs = 2471 no. arc points = 16844 no. surface atoms = 854 nbur = 1144 mkacc time = 6.0000002E-02 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 = 1.456000 m= 223 mr = 2587 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1715 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 5765 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9572199E-09 -2.4535571E-09 midg,1,midg; midg,igrid,midg 3.4222667E-09 -1.3441709E-09 1,midg,midg; igrid,midg,midg 1.3653201E-09 9.2345148E-10 gauss-seidel spectral radius is 0.9853694 estimated iterations to convergence 68 setup time was (sec) 0.3500000 now iterating at: 13:30:37 rms-change max change #iterations 9.0383507E-02 18.49674 at 10iterations 7.4975709E-03 1.426617 at 20iterations 6.3574471E-04 0.1130390 at 30iterations 5.1087107E-05 8.6708069E-03 at 40iterations 4.3378709E-06 8.2302094E-04 at 50iterations finished qdiffx linear iterations at : 13:30:40 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 4.3378709E-06 8.2302094E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 13:30:41 3.435u 0.204s 0:03.98 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 Sat Oct 15 2011 at 13:30:41 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: 234 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1998 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.787418 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): -24.91000 34.84100 ymin,ymax (A): -18.50200 20.24600 zmin,zma (A): -4.089000 38.84700 x,y,z range (A): 59.75100 38.74800 42.93600 scale (grids/A): 1.787418 object centre (A): 4.965502 0.8720007 17.37900 number of atom coordinates read : 1998 total number of charged atoms : 1846 net assigned charge : 3.000005 assigned positive charge : 291.2149 centred at (gu) : 90.00484 90.41420 91.34826 assigned negative charge : -288.2153 centred at (gu) : 90.03315 90.71916 91.76416 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 50768 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16844 grid for indexing accessible points = 1.400000 m= 17588 mr = 34783 m= 2360 mr = 13197 m= 103 mr = 1427 m= 0 mr = 31 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 442 time to turn everything in is 0.2500000 number of dielectric boundary points 21381 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 14430 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) : 0.5958059 object centre at (A) : 4.965502 0.8720007 17.37900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0063835E-03 -5.7410244E-03 midg,1,midg; midg,igrid,midg 7.5084553E-03 -3.4051151E-03 1,midg,midg; igrid,midg,midg 3.4562226E-02 2.8625019E-02 gauss-seidel spectral radius is 0.9983752 estimated iterations to convergence 197 setup time was (sec) 0.4700000 now iterating at: 13:30:41 rms-change max change #iterations 3.169393 153.0931 at 10iterations 1.382376 52.55962 at 20iterations 0.6050764 24.40074 at 30iterations 0.2632085 10.27951 at 40iterations 0.1148644 4.306728 at 50iterations 5.0401833E-02 1.888191 at 60iterations 2.2013927E-02 0.8736129 at 70iterations 9.6320473E-03 0.3377533 at 80iterations 4.2219190E-03 0.1676164 at 90iterations 1.8438809E-03 7.1577072E-02 at 100iterations 8.0620748E-04 3.3152580E-02 at 110iterations 3.5160786E-04 1.3301849E-02 at 120iterations finished qdiffx linear iterations at : 13:30:49 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 3.5160786E-04 1.3301849E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 13:30:49 7.743u 0.222s 0:08.24 96.6% 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 Sat Oct 15 2011 at 13:30:49 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: 234 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1998 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.681127 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): -24.91000 34.84100 ymin,ymax (A): -18.50200 20.24600 zmin,zma (A): -4.089000 38.84700 x,y,z range (A): 59.75100 38.74800 42.93600 scale (grids/A): 2.681127 object centre (A): 4.965502 0.8720007 17.37900 number of atom coordinates read : 1998 total number of charged atoms : 1846 net assigned charge : 3.000005 assigned positive charge : 291.2149 centred at (gu) : 90.00723 90.62130 92.02231 assigned negative charge : -288.2153 centred at (gu) : 90.04967 91.07879 92.64633 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 117286 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16844 grid for indexing accessible points = 1.400000 m= 58140 mr = 84288 m= 19981 mr = 47798 m= 4064 mr = 16320 m= 383 mr = 2999 m= 23 mr = 219 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1292 time to turn everything in is 0.6500000 number of dielectric boundary points 48237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 14765 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) : 1.787418 object centre at (A) : 4.965502 0.8720007 17.37900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.1802428E-02 -4.4662997E-02 midg,1,midg; midg,igrid,midg 6.7520916E-02 -3.5443045E-02 1,midg,midg; igrid,midg,midg 0.4147812 0.4326208 gauss-seidel spectral radius is 0.9991640 estimated iterations to convergence 273 setup time was (sec) 0.9000000 now iterating at: 13:30:50 rms-change max change #iterations 7.664582 277.7791 at 10iterations 4.323502 123.3332 at 20iterations 2.421890 84.10197 at 30iterations 1.347240 37.40452 at 40iterations 0.7465829 16.69969 at 50iterations 0.4150912 9.280849 at 60iterations 0.2305670 5.177853 at 70iterations 0.1280431 3.192232 at 80iterations 7.0847057E-02 1.549955 at 90iterations 3.9421741E-02 0.9843216 at 100iterations 2.1826111E-02 0.5054398 at 110iterations 1.2086870E-02 0.2763062 at 120iterations 6.6968198E-03 0.1463318 at 130iterations 3.6999355E-03 8.4035158E-02 at 140iterations 2.0544245E-03 4.6352386E-02 at 150iterations 1.1387176E-03 2.6011467E-02 at 160iterations 6.2960811E-04 1.3272285E-02 at 170iterations 3.4893528E-04 7.4367523E-03 at 180iterations finished qdiffx linear iterations at : 13:31:01 total time elapsed so far: 12.04000 # loops : 180 mean,max change (kT/e) : 3.4893528E-04 7.4367523E-03 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.16000 DelPhi exited at 13:31:02 12.167u 0.199s 0:12.63 97.7% 0+0k 0+0io 0pf+0w