Tue Oct 11 06:16:23 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 06:16:23 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2303 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: ZN7 730 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7325103 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): 25.56600 72.17700 ymin,ymax (A): -18.85400 29.74600 zmin,zma (A): 3.760000 46.13800 x,y,z range (A): 46.61100 48.60000 42.37800 scale (grids/A): 0.7325103 object centre (A): 48.87150 5.446000 24.94900 number of atom coordinates read : 2303 total number of charged atoms : 1975 net assigned charge : 7.031008 assigned positive charge : 322.5440 centred at (gu) : 89.17738 90.78145 90.43325 assigned negative charge : -315.5131 centred at (gu) : 89.32142 90.72953 90.49947 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7760 nv = 96 ne = 84 npr = 42180 no. pairs analyzed = 42180 no. exposed pairs = 2571 no. arc points = 17318 no. surface atoms = 880 nbur = 1423 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 532 mr = 4540 m= 1 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1519 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8216 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4800266E-07 5.0320001E-08 midg,1,midg; midg,igrid,midg 5.1766936E-08 1.7147930E-07 1,midg,midg; igrid,midg,midg 2.6377361E-07 -1.7293935E-08 gauss-seidel spectral radius is 0.9902805 estimated iterations to convergence 82 setup time was (sec) 0.5300000 now iterating at: 06:16:24 rms-change max change #iterations 0.2379346 31.63475 at 10iterations 3.1538073E-02 4.155368 at 20iterations 4.4746106E-03 0.6209679 at 30iterations 8.0777059E-04 9.7991943E-02 at 40iterations 2.1348422E-04 2.4391174E-02 at 50iterations finished qdiffx linear iterations at : 06:16:27 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 2.1348422E-04 2.4391174E-02 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 06:16:28 4.107u 0.225s 0:04.62 93.5% 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 06:16:28 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2303 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: ZN7 730 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.197531 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): 25.56600 72.17700 ymin,ymax (A): -18.85400 29.74600 zmin,zma (A): 3.760000 46.13800 x,y,z range (A): 46.61100 48.60000 42.37800 scale (grids/A): 2.197531 object centre (A): 48.87150 5.446000 24.94900 number of atom coordinates read : 2303 total number of charged atoms : 1975 net assigned charge : 7.031008 assigned positive charge : 322.5440 centred at (gu) : 87.53220 92.34410 91.29994 assigned negative charge : -315.5131 centred at (gu) : 87.96426 92.18874 91.49842 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81383 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17318 grid for indexing accessible points = 1.400000 m= 34175 mr = 58436 m= 7133 mr = 26450 m= 702 mr = 4868 m= 26 mr = 370 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 33295 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15700 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) : 0.7325103 object centre at (A) : 48.87150 5.446000 24.94900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6400322E-02 3.7443172E-02 midg,1,midg; midg,igrid,midg 4.8836447E-02 4.2088374E-02 1,midg,midg; igrid,midg,midg 5.8555838E-02 -5.9758235E-02 gauss-seidel spectral radius is 0.9988984 estimated iterations to convergence 238 setup time was (sec) 0.9700000 now iterating at: 06:16:29 rms-change max change #iterations 4.945956 184.7071 at 10iterations 2.501191 80.85502 at 20iterations 1.271351 37.08240 at 30iterations 0.6420097 19.27686 at 40iterations 0.3251451 9.664750 at 50iterations 0.1654366 4.769553 at 60iterations 8.3793946E-02 2.451619 at 70iterations 4.2724010E-02 1.180099 at 80iterations 2.1812558E-02 0.5709786 at 90iterations 1.1200918E-02 0.3206086 at 100iterations 5.7995045E-03 0.1624146 at 110iterations 3.0717251E-03 8.9466095E-02 at 120iterations finished qdiffx linear iterations at : 06:16:37 total time elapsed so far: 9.380000 # loops : 120 mean,max change (kT/e) : 3.0717251E-03 8.9466095E-02 energy calculations done at 9.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 06:16:38 9.556u 0.266s 0:10.38 94.5% 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 06:16:38 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2303 !!! WARNING: HIZ 57 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: ZN7 730 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.296296 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): 25.56600 72.17700 ymin,ymax (A): -18.85400 29.74600 zmin,zma (A): 3.760000 46.13800 x,y,z range (A): 46.61100 48.60000 42.37800 scale (grids/A): 3.296296 object centre (A): 48.87150 5.446000 24.94900 number of atom coordinates read : 2303 total number of charged atoms : 1975 net assigned charge : 7.031008 assigned positive charge : 322.5440 centred at (gu) : 86.29822 93.51630 91.94982 assigned negative charge : -315.5131 centred at (gu) : 86.94640 93.28301 92.24771 start vw surface at 0.1500000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 187319 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17318 grid for indexing accessible points = 1.400000 m= 104672 mr = 140297 m= 45023 mr = 87924 m= 13720 mr = 37444 m= 2854 mr = 10767 m= 432 mr = 2101 m= 33 mr = 291 m= 0 mr = 9 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.110000 number of dielectric boundary points 75220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.250000 number of grid points assigned charge 15800 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) : 2.197531 object centre at (A) : 48.87150 5.446000 24.94900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1281349 0.3273860 midg,1,midg; midg,igrid,midg 0.3574430 0.2176531 1,midg,midg; igrid,midg,midg 0.5308794 -0.6768964 gauss-seidel spectral radius is 0.9993141 estimated iterations to convergence 301 setup time was (sec) 2.450000 now iterating at: 06:16:41 rms-change max change #iterations 10.86020 294.7226 at 10iterations 6.478548 135.4449 at 20iterations 3.858056 81.01875 at 30iterations 2.297933 46.13015 at 40iterations 1.364148 26.63174 at 50iterations 0.8086188 16.69081 at 60iterations 0.4785156 9.505900 at 70iterations 0.2830249 4.868691 at 80iterations 0.1672165 3.309678 at 90iterations 9.8844752E-02 1.649206 at 100iterations 5.8586586E-02 0.9490128 at 110iterations 3.4925729E-02 0.5908203 at 120iterations 2.0940498E-02 0.3497353 at 130iterations 1.2828142E-02 0.2216949 at 140iterations 8.1011215E-03 0.1475601 at 150iterations 5.3503122E-03 0.1071472 at 160iterations 3.7466204E-03 7.2723389E-02 at 170iterations 2.7938725E-03 5.2221298E-02 at 180iterations finished qdiffx linear iterations at : 06:16:54 total time elapsed so far: 15.74000 # loops : 180 mean,max change (kT/e) : 2.7938725E-03 5.2221298E-02 energy calculations done at 15.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.92000 DelPhi exited at 06:16:55 15.917u 0.253s 0:16.63 97.1% 0+0k 0+0io 0pf+0w