Tue Oct 11 08:00:31 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 Tue Oct 11 2011 at 08:00:31 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2288 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.6591372 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): -57.99000 -3.980000 ymin,ymax (A): 64.01200 108.3240 zmin,zma (A): -24.93200 19.25700 x,y,z range (A): 54.01000 44.31200 44.18900 scale (grids/A): 0.6591372 object centre (A): -30.98500 86.16800 -2.837500 number of atom coordinates read : 2288 total number of charged atoms : 2150 net assigned charge : 3.525007 assigned positive charge : 341.6627 centred at (gu) : 91.04548 91.06809 90.45975 assigned negative charge : -338.1379 centred at (gu) : 91.20573 91.23691 90.42418 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6553 nv = 96 ne = 84 npr = 47207 no. pairs analyzed = 47207 no. exposed pairs = 2681 no. arc points = 18875 no. surface atoms = 915 nbur = 1373 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 379 mr = 3731 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.3300000 number of dielectric boundary points 3154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1855 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7802 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1358272E-09 1.6900866E-08 midg,1,midg; midg,igrid,midg 2.9847971E-08 -2.4634316E-08 1,midg,midg; igrid,midg,midg 2.8873274E-08 -2.2646434E-08 gauss-seidel spectral radius is 0.9880387 estimated iterations to convergence 75 setup time was (sec) 0.6600000 now iterating at: 08:00:32 rms-change max change #iterations 0.1563952 23.12394 at 10iterations 1.6902903E-02 2.442719 at 20iterations 1.7989710E-03 0.2772417 at 30iterations 1.8746794E-04 2.8640747E-02 at 40iterations 1.9985127E-05 2.8610229E-03 at 50iterations finished qdiffx linear iterations at : 08:00:36 total time elapsed so far: 4.150000 # loops : 50 mean,max change (kT/e) : 1.9985127E-05 2.8610229E-03 energy calculations done at 4.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 08:00:36 4.372u 0.422s 0:05.14 93.1% 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 Tue Oct 11 2011 at 08:00:36 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2288 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 1.977412 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): -57.99000 -3.980000 ymin,ymax (A): 64.01200 108.3240 zmin,zma (A): -24.93200 19.25700 x,y,z range (A): 54.01000 44.31200 44.18900 scale (grids/A): 1.977412 object centre (A): -30.98500 86.16800 -2.837500 number of atom coordinates read : 2288 total number of charged atoms : 2150 net assigned charge : 3.525007 assigned positive charge : 341.6627 centred at (gu) : 93.13654 93.20422 91.37898 assigned negative charge : -338.1379 centred at (gu) : 93.61724 93.71067 91.27247 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 70321 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18875 grid for indexing accessible points = 1.400000 m= 26348 mr = 49354 m= 4504 mr = 19907 m= 289 mr = 2931 m= 8 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2905 time to turn everything in is 0.7200000 number of dielectric boundary points 29137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 16994 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) : 0.6591372 object centre at (A) : -30.98500 86.16800 -2.837500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9041181E-02 2.1682302E-02 midg,1,midg; midg,igrid,midg 2.2211896E-02 -2.6650829E-02 1,midg,midg; igrid,midg,midg 5.1516723E-02 1.9731460E-02 gauss-seidel spectral radius is 0.9986955 estimated iterations to convergence 219 setup time was (sec) 1.050000 now iterating at: 08:00:38 rms-change max change #iterations 4.195920 186.0983 at 10iterations 1.998265 66.53645 at 20iterations 0.9567114 31.30151 at 30iterations 0.4556751 15.48909 at 40iterations 0.2173345 6.974529 at 50iterations 0.1035685 3.136145 at 60iterations 4.9484283E-02 1.599304 at 70iterations 2.3649760E-02 0.7865076 at 80iterations 1.1250569E-02 0.3955154 at 90iterations 5.3461310E-03 0.1734300 at 100iterations 2.5485936E-03 7.7828169E-02 at 110iterations 1.2234142E-03 3.7001967E-02 at 120iterations finished qdiffx linear iterations at : 08:00:47 total time elapsed so far: 9.960000 # loops : 120 mean,max change (kT/e) : 1.2234142E-03 3.7001967E-02 energy calculations done at 9.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.19000 DelPhi exited at 08:00:48 10.190u 0.455s 0:11.01 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 Tue Oct 11 2011 at 08:00:48 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2288 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.966117 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): -57.99000 -3.980000 ymin,ymax (A): 64.01200 108.3240 zmin,zma (A): -24.93200 19.25700 x,y,z range (A): 54.01000 44.31200 44.18900 scale (grids/A): 2.966117 object centre (A): -30.98500 86.16800 -2.837500 number of atom coordinates read : 2288 total number of charged atoms : 2150 net assigned charge : 3.525007 assigned positive charge : 341.6627 centred at (gu) : 94.70481 94.80625 92.06838 assigned negative charge : -338.1379 centred at (gu) : 95.42586 95.56596 91.90878 start vw surface at 0.1400000 fill in re-entrant regions at 0.6200000 boundary points on vw surface= 162305 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18875 grid for indexing accessible points = 1.400000 m= 83741 mr = 118762 m= 32032 mr = 69509 m= 8438 mr = 26406 m= 1259 mr = 6470 m= 140 mr = 870 m= 12 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 9624 time to turn everything in is 1.890000 number of dielectric boundary points 65804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 17196 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) : 1.977412 object centre at (A) : -30.98500 86.16800 -2.837500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2875988 0.2537838 midg,1,midg; midg,igrid,midg 0.1867037 -0.3840852 1,midg,midg; igrid,midg,midg 0.6939137 0.3349608 gauss-seidel spectral radius is 0.9992607 estimated iterations to convergence 290 setup time was (sec) 2.230000 now iterating at: 08:00:50 rms-change max change #iterations 9.690526 425.3445 at 10iterations 5.608754 155.2659 at 20iterations 3.244687 65.80717 at 30iterations 1.870570 35.61389 at 40iterations 1.078851 19.27288 at 50iterations 0.6208964 11.21981 at 60iterations 0.3575401 6.949073 at 70iterations 0.2057887 3.803092 at 80iterations 0.1183900 2.137183 at 90iterations 6.8052784E-02 1.182419 at 100iterations 3.9186489E-02 0.7041740 at 110iterations 2.2555387E-02 0.3944650 at 120iterations 1.2974835E-02 0.2617664 at 130iterations 7.4976962E-03 0.1372147 at 140iterations 4.3084752E-03 7.4810028E-02 at 150iterations 2.4982374E-03 4.6257019E-02 at 160iterations 1.4497710E-03 2.6222229E-02 at 170iterations 8.4890099E-04 1.8379211E-02 at 180iterations finished qdiffx linear iterations at : 08:01:05 total time elapsed so far: 16.87000 # loops : 180 mean,max change (kT/e) : 8.4890099E-04 1.8379211E-02 energy calculations done at 16.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.08000 DelPhi exited at 08:01:05 17.088u 0.498s 0:17.87 98.3% 0+0k 0+0io 0pf+0w