Sat Oct 8 14:14:24 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 Sat Oct 8 2011 at 14:14:24 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2952 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6183884 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): -11.42000 43.21400 ymin,ymax (A): 9.849999 55.21300 zmin,zma (A): 36.50100 94.07000 x,y,z range (A): 54.63400 45.36300 57.56900 scale (grids/A): 0.6183884 object centre (A): 15.89700 32.53150 65.28550 number of atom coordinates read : 2952 total number of charged atoms : 2805 net assigned charge : -1.985993 assigned positive charge : 442.6256 centred at (gu) : 89.16835 89.84135 91.36533 assigned negative charge : -444.6124 centred at (gu) : 89.11124 89.74123 91.33762 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7552 nv = 96 ne = 84 npr = 60951 no. pairs analyzed = 60951 no. exposed pairs = 3438 no. arc points = 23654 no. surface atoms = 1170 nbur = 1782 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 372 mr = 4391 m= 1 mr = 43 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 0.3700000 number of dielectric boundary points 3491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2371 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 9298 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6037974E-09 7.2949424E-10 midg,1,midg; midg,igrid,midg -9.1499892E-09 5.4817337E-09 1,midg,midg; igrid,midg,midg -6.8118120E-09 2.1630231E-09 gauss-seidel spectral radius is 0.9864854 estimated iterations to convergence 70 setup time was (sec) 0.8100000 now iterating at: 14:14:25 rms-change max change #iterations 0.1384594 23.12811 at 10iterations 1.3265895E-02 1.762421 at 20iterations 1.4049362E-03 0.2255058 at 30iterations 2.0677228E-04 2.8900146E-02 at 40iterations 4.2311276E-05 6.5116882E-03 at 50iterations finished qdiffx linear iterations at : 14:14:31 total time elapsed so far: 7.020000 # loops : 50 mean,max change (kT/e) : 4.2311276E-05 6.5116882E-03 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.200000 DelPhi exited at 14:14:32 7.202u 0.655s 0:08.15 96.3% 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 Sat Oct 8 2011 at 14:14:32 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2952 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.855165 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): -11.42000 43.21400 ymin,ymax (A): 9.849999 55.21300 zmin,zma (A): 36.50100 94.07000 x,y,z range (A): 54.63400 45.36300 57.56900 scale (grids/A): 1.855165 object centre (A): 15.89700 32.53150 65.28550 number of atom coordinates read : 2952 total number of charged atoms : 2805 net assigned charge : -1.985993 assigned positive charge : 442.6256 centred at (gu) : 87.50447 89.52330 94.09575 assigned negative charge : -444.6124 centred at (gu) : 87.33376 89.22328 94.01260 start vw surface at 0.1400000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 83207 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23654 grid for indexing accessible points = 1.400000 m= 30559 mr = 60328 m= 4555 mr = 23181 m= 216 mr = 2776 m= 0 mr = 56 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 142 time to turn everything in is 0.7700000 number of dielectric boundary points 32196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 22001 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) : 0.6183884 object centre at (A) : 15.89700 32.53150 65.28550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1285481E-02 5.4172305E-03 midg,1,midg; midg,igrid,midg -2.7567251E-03 1.4093032E-02 1,midg,midg; igrid,midg,midg -4.4574063E-02 2.0629028E-03 gauss-seidel spectral radius is 0.9985970 estimated iterations to convergence 212 setup time was (sec) 1.260000 now iterating at: 14:14:34 rms-change max change #iterations 4.408163 179.1036 at 10iterations 2.036895 62.34057 at 20iterations 0.9492949 30.11871 at 30iterations 0.4393303 16.04568 at 40iterations 0.2045080 7.454834 at 50iterations 9.5100857E-02 2.967056 at 60iterations 4.4060450E-02 1.277363 at 70iterations 2.0439452E-02 0.6365891 at 80iterations 9.5333876E-03 0.2871928 at 90iterations 4.4552106E-03 0.1364212 at 100iterations 2.0857332E-03 6.0726166E-02 at 110iterations 9.7870559E-04 2.8932571E-02 at 120iterations finished qdiffx linear iterations at : 14:14:50 total time elapsed so far: 17.24000 # loops : 120 mean,max change (kT/e) : 9.7870559E-04 2.8932571E-02 energy calculations done at 17.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.41000 DelPhi exited at 14:14:51 17.415u 0.733s 0:18.46 98.2% 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 8 2011 at 14:14:51 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2952 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 316 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.782748 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): -11.42000 43.21400 ymin,ymax (A): 9.849999 55.21300 zmin,zma (A): 36.50100 94.07000 x,y,z range (A): 54.63400 45.36300 57.56900 scale (grids/A): 2.782748 object centre (A): 15.89700 32.53150 65.28550 number of atom coordinates read : 2952 total number of charged atoms : 2805 net assigned charge : -1.985993 assigned positive charge : 442.6256 centred at (gu) : 86.25655 89.28490 96.14355 assigned negative charge : -444.6124 centred at (gu) : 86.00038 88.83498 96.01874 start vw surface at 0.1300000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 192759 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23654 grid for indexing accessible points = 1.400000 m= 99832 mr = 145516 m= 35527 mr = 83602 m= 8022 mr = 28911 m= 1013 mr = 5935 m= 37 mr = 671 m= 0 mr = 9 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 452 time to turn everything in is 1.960000 number of dielectric boundary points 72546 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.190000 number of grid points assigned charge 22439 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) : 1.855165 object centre at (A) : 15.89700 32.53150 65.28550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9904511E-02 0.1034945 midg,1,midg; midg,igrid,midg -1.4912256E-02 0.1641248 1,midg,midg; igrid,midg,midg -0.5464641 0.1521422 gauss-seidel spectral radius is 0.9992518 estimated iterations to convergence 289 setup time was (sec) 2.530000 now iterating at: 14:14:54 rms-change max change #iterations 10.33236 322.7313 at 10iterations 6.051140 132.5088 at 20iterations 3.499298 75.98850 at 30iterations 2.028935 39.88112 at 40iterations 1.174777 22.62354 at 50iterations 0.6769206 13.75623 at 60iterations 0.3883922 6.992992 at 70iterations 0.2236398 4.203478 at 80iterations 0.1283544 2.315568 at 90iterations 7.3870890E-02 1.390226 at 100iterations 4.2361144E-02 0.7540722 at 110iterations 2.4375219E-02 0.4095039 at 120iterations 1.3973230E-02 0.2639542 at 130iterations 8.0370801E-03 0.1430717 at 140iterations 4.6306080E-03 8.0398560E-02 at 150iterations 2.6747750E-03 4.4976234E-02 at 160iterations 1.5510812E-03 2.8121948E-02 at 170iterations 9.0800622E-04 1.6628265E-02 at 180iterations finished qdiffx linear iterations at : 14:15:20 total time elapsed so far: 29.04000 # loops : 180 mean,max change (kT/e) : 9.0800622E-04 1.6628265E-02 energy calculations done at 29.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.21000 DelPhi exited at 14:15:21 29.217u 0.776s 0:30.24 99.1% 0+0k 0+0io 0pf+0w