Sat Oct 15 10:22:51 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 10:22:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4417 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: 0.5779971 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): -27.35300 34.23900 ymin,ymax (A): 35.31900 95.00500 zmin,zma (A): 30.95800 89.37500 x,y,z range (A): 61.59200 59.68600 58.41700 scale (grids/A): 0.5779971 object centre (A): 3.443001 65.16200 60.16650 number of atom coordinates read : 4417 total number of charged atoms : 4256 net assigned charge : -8.499952 assigned positive charge : 663.2980 centred at (gu) : 90.77161 88.99034 89.14167 assigned negative charge : -671.8013 centred at (gu) : 90.62312 89.03765 89.30138 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9456 nv = 96 ne = 84 npr = 92825 no. pairs analyzed = 92825 no. exposed pairs = 4971 no. arc points = 33290 no. surface atoms = 1676 nbur = 2741 mkacc time = 0.2000000 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 = 1.484000 m= 409 mr = 5537 m= 4 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 116 time to turn everything in is 0.4300000 number of dielectric boundary points 4290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3484 ## 399 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 12392 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7649572E-09 -5.6264211E-09 midg,1,midg; midg,igrid,midg -4.3577766E-10 -2.6145086E-09 1,midg,midg; igrid,midg,midg -5.4405129E-09 3.2800247E-09 gauss-seidel spectral radius is 0.9846534 estimated iterations to convergence 66 setup time was (sec) 0.6700000 now iterating at: 10:22:52 rms-change max change #iterations 0.1226056 16.76437 at 10iterations 9.8298183E-03 1.357904 at 20iterations 1.0354560E-03 0.1303577 at 30iterations 2.2171554E-04 2.5058746E-02 at 40iterations 7.4800366E-05 9.1428757E-03 at 50iterations finished qdiffx linear iterations at : 10:22:55 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 7.4800366E-05 9.1428757E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 10:22:55 3.561u 0.206s 0:04.17 90.1% 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 Sat Oct 15 2011 at 10:22:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4417 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.733991 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): -27.35300 34.23900 ymin,ymax (A): 35.31900 95.00500 zmin,zma (A): 30.95800 89.37500 x,y,z range (A): 61.59200 59.68600 58.41700 scale (grids/A): 1.733991 object centre (A): 3.443001 65.16200 60.16650 number of atom coordinates read : 4417 total number of charged atoms : 4256 net assigned charge : -8.499952 assigned positive charge : 663.2980 centred at (gu) : 92.31344 86.96955 87.42359 assigned negative charge : -671.8013 centred at (gu) : 91.86903 87.11246 87.90372 start vw surface at 0.1800000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 105945 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33290 grid for indexing accessible points = 1.400000 m= 36300 mr = 77549 m= 4670 mr = 26993 m= 164 mr = 2865 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 6236 time to turn everything in is 0.7100000 number of dielectric boundary points 39626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 342 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 33023 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) : 0.5779971 object centre at (A) : 3.443001 65.16200 60.16650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5941124E-02 -3.2417331E-02 midg,1,midg; midg,igrid,midg 1.1923056E-02 -2.1030584E-02 1,midg,midg; igrid,midg,midg -3.8764190E-02 3.4315482E-02 gauss-seidel spectral radius is 0.9985170 estimated iterations to convergence 206 setup time was (sec) 1.010000 now iterating at: 10:22:57 rms-change max change #iterations 4.796465 172.8024 at 10iterations 2.164303 67.25365 at 20iterations 0.9850631 28.48503 at 30iterations 0.4469874 12.76965 at 40iterations 0.2030441 6.146442 at 50iterations 9.2483409E-02 2.510921 at 60iterations 4.2113066E-02 1.198023 at 70iterations 1.9188946E-02 0.5317383 at 80iterations 8.7777283E-03 0.2462006 at 90iterations 4.0134103E-03 0.1093311 at 100iterations 1.8541104E-03 5.3749084E-02 at 110iterations 8.7399938E-04 2.3612022E-02 at 120iterations finished qdiffx linear iterations at : 10:23:04 total time elapsed so far: 8.010000 # loops : 120 mean,max change (kT/e) : 8.7399938E-04 2.3612022E-02 energy calculations done at 8.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.190000 DelPhi exited at 10:23:04 8.188u 0.250s 0:08.83 95.4% 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 Sat Oct 15 2011 at 10:23:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4417 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.600987 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): -27.35300 34.23900 ymin,ymax (A): 35.31900 95.00500 zmin,zma (A): 30.95800 89.37500 x,y,z range (A): 61.59200 59.68600 58.41700 scale (grids/A): 2.600987 object centre (A): 3.443001 65.16200 60.16650 number of atom coordinates read : 4417 total number of charged atoms : 4256 net assigned charge : -8.499952 assigned positive charge : 663.2980 centred at (gu) : 93.46974 85.45406 86.13495 assigned negative charge : -671.8013 centred at (gu) : 92.80329 85.66862 86.85562 start vw surface at 0.1700000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 246301 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33290 grid for indexing accessible points = 1.400000 m= 122976 mr = 187929 m= 39223 mr = 101949 m= 7944 mr = 31381 m= 749 mr = 6025 m= 12 mr = 458 m= 0 mr = 0 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 20806 time to turn everything in is 1.790000 number of dielectric boundary points 89463 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 34031 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) : 1.733991 object centre at (A) : 3.443001 65.16200 60.16650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6395729 -0.3757303 midg,1,midg; midg,igrid,midg 0.2596698 -0.4313394 1,midg,midg; igrid,midg,midg -0.3864329 0.3707809 gauss-seidel spectral radius is 0.9992521 estimated iterations to convergence 289 setup time was (sec) 2.140000 now iterating at: 10:23:07 rms-change max change #iterations 11.67390 332.0355 at 10iterations 6.825525 138.5631 at 20iterations 3.948889 70.94450 at 30iterations 2.287659 37.75974 at 40iterations 1.318520 26.95559 at 50iterations 0.7600818 12.63287 at 60iterations 0.4395134 7.458332 at 70iterations 0.2522076 4.316926 at 80iterations 0.1448834 2.470822 at 90iterations 8.3373360E-02 1.427287 at 100iterations 4.7892164E-02 0.8493824 at 110iterations 2.7581749E-02 0.4557781 at 120iterations 1.5875367E-02 0.2573242 at 130iterations 9.1541670E-03 0.1477852 at 140iterations 5.3193048E-03 8.1607819E-02 at 150iterations 3.1133569E-03 4.9255371E-02 at 160iterations 1.8552173E-03 3.2958984E-02 at 170iterations 1.1373811E-03 2.1591187E-02 at 180iterations finished qdiffx linear iterations at : 10:23:19 total time elapsed so far: 13.81000 # loops : 180 mean,max change (kT/e) : 1.1373811E-03 2.1591187E-02 energy calculations done at 13.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.98000 DelPhi exited at 10:23:19 13.980u 0.278s 0:14.60 97.6% 0+0k 0+0io 0pf+0w