Sat Oct 8 20:27:58 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 20:27:58 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 119 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7243134 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): -6.312000 42.24400 ymin,ymax (A): -2.292000 46.85800 zmin,zma (A): -8.420000 39.91300 x,y,z range (A): 48.55600 49.15000 48.33300 scale (grids/A): 0.7243134 object centre (A): 17.96600 22.28300 15.74650 number of atom coordinates read : 2567 total number of charged atoms : 2437 net assigned charge : 3.434007 assigned positive charge : 390.1280 centred at (gu) : 88.35045 91.52612 90.83324 assigned negative charge : -386.6946 centred at (gu) : 88.25040 91.66029 90.72951 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8994 nv = 96 ne = 84 npr = 54018 no. pairs analyzed = 54018 no. exposed pairs = 2933 no. arc points = 21047 no. surface atoms = 980 nbur = 1587 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 591 mr = 5244 m= 4 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 549 time to turn everything in is 0.3000000 number of dielectric boundary points 4204 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1865 ## 139 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 10105 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9291077E-08 1.5952780E-07 midg,1,midg; midg,igrid,midg 1.2113118E-07 -1.0118987E-07 1,midg,midg; igrid,midg,midg -6.1229628E-08 9.7014727E-08 gauss-seidel spectral radius is 0.9901071 estimated iterations to convergence 82 setup time was (sec) 0.5700000 now iterating at: 20:27:59 rms-change max change #iterations 0.2531289 30.79486 at 10iterations 3.3404600E-02 3.598020 at 20iterations 4.3036179E-03 0.5677490 at 30iterations 5.5674941E-04 6.6377640E-02 at 40iterations 7.2752766E-05 1.0913849E-02 at 50iterations finished qdiffx linear iterations at : 20:28:03 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 7.2752766E-05 1.0913849E-02 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 20:28:03 4.198u 0.236s 0:04.69 94.2% 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 20:28:03 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 119 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.172940 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): -6.312000 42.24400 ymin,ymax (A): -2.292000 46.85800 zmin,zma (A): -8.420000 39.91300 x,y,z range (A): 48.55600 49.15000 48.33300 scale (grids/A): 2.172940 object centre (A): 17.96600 22.28300 15.74650 number of atom coordinates read : 2567 total number of charged atoms : 2437 net assigned charge : 3.434007 assigned positive charge : 390.1280 centred at (gu) : 85.05095 94.57802 92.49928 assigned negative charge : -386.6946 centred at (gu) : 84.75086 94.98053 92.18817 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 95943 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21047 grid for indexing accessible points = 1.400000 m= 37887 mr = 68451 m= 7677 mr = 29418 m= 800 mr = 5482 m= 22 mr = 478 m= 0 mr = 1 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 14416 time to turn everything in is 0.7000000 number of dielectric boundary points 38499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 19403 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) : 0.7243134 object centre at (A) : 17.96600 22.28300 15.74650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7543703E-04 3.8599193E-02 midg,1,midg; midg,igrid,midg 9.6825678E-03 -7.4491389E-02 1,midg,midg; igrid,midg,midg -1.6603282E-02 0.1103877 gauss-seidel spectral radius is 0.9989170 estimated iterations to convergence 240 setup time was (sec) 1.030000 now iterating at: 20:28:04 rms-change max change #iterations 5.436046 216.7159 at 10iterations 2.759379 91.18800 at 20iterations 1.399821 39.19598 at 30iterations 0.7132334 20.75079 at 40iterations 0.3628803 9.266333 at 50iterations 0.1847838 4.962130 at 60iterations 9.3798280E-02 2.779594 at 70iterations 4.7851723E-02 1.269318 at 80iterations 2.4367359E-02 0.6839849 at 90iterations 1.2340432E-02 0.2971268 at 100iterations 6.3098278E-03 0.1691971 at 110iterations 3.2162543E-03 7.9956055E-02 at 120iterations finished qdiffx linear iterations at : 20:28:13 total time elapsed so far: 9.630000 # loops : 120 mean,max change (kT/e) : 3.2162543E-03 7.9956055E-02 energy calculations done at 9.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.810000 DelPhi exited at 20:28:14 9.815u 0.272s 0:10.40 96.9% 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 20:28:14 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2567 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 119 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.259410 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): -6.312000 42.24400 ymin,ymax (A): -2.292000 46.85800 zmin,zma (A): -8.420000 39.91300 x,y,z range (A): 48.55600 49.15000 48.33300 scale (grids/A): 3.259410 object centre (A): 17.96600 22.28300 15.74650 number of atom coordinates read : 2567 total number of charged atoms : 2437 net assigned charge : 3.434007 assigned positive charge : 390.1280 centred at (gu) : 82.57628 96.86668 93.74887 assigned negative charge : -386.6946 centred at (gu) : 82.12629 97.47059 93.28219 start vw surface at 0.1500000 fill in re-entrant regions at 1.040000 boundary points on vw surface= 221189 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21047 grid for indexing accessible points = 1.400000 m= 118019 mr = 164365 m= 48434 mr = 99612 m= 14909 mr = 40618 m= 3332 mr = 12056 m= 436 mr = 2606 m= 22 mr = 327 m= 0 mr = 4 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 48516 time to turn everything in is 2.340000 number of dielectric boundary points 86753 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.490000 number of grid points assigned charge 19496 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) : 2.172940 object centre at (A) : 17.96600 22.28300 15.74650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2094637 0.2170240 midg,1,midg; midg,igrid,midg -5.5729419E-02 -0.5044613 1,midg,midg; igrid,midg,midg -0.1742338 1.636718 gauss-seidel spectral radius is 0.9993255 estimated iterations to convergence 304 setup time was (sec) 2.690000 now iterating at: 20:28:17 rms-change max change #iterations 11.76080 358.0517 at 10iterations 6.931370 134.0916 at 20iterations 4.087679 74.77119 at 30iterations 2.399380 35.83668 at 40iterations 1.413439 23.38934 at 50iterations 0.8343113 13.35803 at 60iterations 0.4910129 7.256612 at 70iterations 0.2888984 4.274558 at 80iterations 0.1699376 2.605106 at 90iterations 0.1001005 1.549096 at 100iterations 5.8789555E-02 0.9284744 at 110iterations 3.4695350E-02 0.5758438 at 120iterations 2.0427557E-02 0.2878332 at 130iterations 1.2014536E-02 0.1824961 at 140iterations 7.0809270E-03 0.1062241 at 150iterations 4.1746208E-03 5.9854507E-02 at 160iterations 2.4621359E-03 3.9503098E-02 at 170iterations 1.4536789E-03 2.2569656E-02 at 180iterations finished qdiffx linear iterations at : 20:28:30 total time elapsed so far: 16.40000 # loops : 180 mean,max change (kT/e) : 1.4536789E-03 2.2569656E-02 energy calculations done at 16.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.58000 DelPhi exited at 20:28:31 16.581u 0.282s 0:17.13 98.4% 0+0k 0+0io 0pf+0w