Sat Oct 15 11:28:34 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 15 2011 at 11:28:34 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 689 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6124204 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): -32.12400 17.63200 ymin,ymax (A): -23.56500 24.14100 zmin,zma (A): -12.56600 45.56400 x,y,z range (A): 49.75600 47.70600 58.13000 scale (grids/A): 0.6124204 object centre (A): -7.246000 0.2879992 16.49900 number of atom coordinates read : 2629 total number of charged atoms : 2480 net assigned charge : 3.406008 assigned positive charge : 396.9350 centred at (gu) : 88.76465 88.92495 89.65588 assigned negative charge : -393.5295 centred at (gu) : 88.66562 88.98123 89.55649 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6428 nv = 96 ne = 84 npr = 54987 no. pairs analyzed = 54987 no. exposed pairs = 3042 no. arc points = 21834 no. surface atoms = 1015 nbur = 1614 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 297 mr = 3568 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 181 time to turn everything in is 0.2000000 number of dielectric boundary points 3122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2234 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8057 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.4473173E-09 6.9580830E-09 midg,1,midg; midg,igrid,midg 6.6585271E-09 -6.2088451E-10 1,midg,midg; igrid,midg,midg -4.2342179E-09 5.6977583E-09 gauss-seidel spectral radius is 0.9861938 estimated iterations to convergence 70 setup time was (sec) 0.4300000 now iterating at: 11:28:35 rms-change max change #iterations 0.1211290 19.03445 at 10iterations 1.0829704E-02 1.649885 at 20iterations 9.8011631E-04 0.1488104 at 30iterations 8.7977984E-05 1.2306213E-02 at 40iterations 7.8992007E-06 1.2875199E-03 at 50iterations finished qdiffx linear iterations at : 11:28:38 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 7.8992007E-06 1.2875199E-03 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 11:28:39 3.987u 0.238s 0:04.75 88.6% 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 Sat Oct 15 2011 at 11:28:39 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 689 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.837261 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): -32.12400 17.63200 ymin,ymax (A): -23.56500 24.14100 zmin,zma (A): -12.56600 45.56400 x,y,z range (A): 49.75600 47.70600 58.13000 scale (grids/A): 1.837261 object centre (A): -7.246000 0.2879992 16.49900 number of atom coordinates read : 2629 total number of charged atoms : 2480 net assigned charge : 3.406008 assigned positive charge : 396.9350 centred at (gu) : 86.29365 86.77439 88.96719 assigned negative charge : -393.5295 centred at (gu) : 85.99654 86.94344 88.66936 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 70372 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21834 grid for indexing accessible points = 1.400000 m= 23927 mr = 49275 m= 3159 mr = 17577 m= 154 mr = 1879 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 6147 time to turn everything in is 0.3800000 number of dielectric boundary points 28840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 19440 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) : 0.6124204 object centre at (A) : -7.246000 0.2879992 16.49900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7353272E-03 2.6257059E-02 midg,1,midg; midg,igrid,midg 1.3596459E-02 -2.0933776E-04 1,midg,midg; igrid,midg,midg -8.0220774E-03 2.8858684E-02 gauss-seidel spectral radius is 0.9985353 estimated iterations to convergence 207 setup time was (sec) 0.6900000 now iterating at: 11:28:40 rms-change max change #iterations 3.949107 167.1632 at 10iterations 1.804518 71.94736 at 20iterations 0.8202510 27.73098 at 30iterations 0.3750823 12.74184 at 40iterations 0.1710128 6.274266 at 50iterations 7.8090467E-02 2.720195 at 60iterations 3.5547968E-02 1.085739 at 70iterations 1.6203232E-02 0.5365276 at 80iterations 7.3954854E-03 0.2398386 at 90iterations 3.3616542E-03 0.1079826 at 100iterations 1.5370082E-03 5.0598145E-02 at 110iterations 7.0048176E-04 2.5485039E-02 at 120iterations finished qdiffx linear iterations at : 11:28:50 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 7.0048176E-04 2.5485039E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.510000 DelPhi exited at 11:28:50 9.510u 0.328s 0:11.28 87.1% 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 11:28:51 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 689 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.755892 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): -32.12400 17.63200 ymin,ymax (A): -23.56500 24.14100 zmin,zma (A): -12.56600 45.56400 x,y,z range (A): 49.75600 47.70600 58.13000 scale (grids/A): 2.755892 object centre (A): -7.246000 0.2879992 16.49900 number of atom coordinates read : 2629 total number of charged atoms : 2480 net assigned charge : 3.406008 assigned positive charge : 396.9350 centred at (gu) : 84.44042 85.16148 88.45051 assigned negative charge : -393.5295 centred at (gu) : 83.99494 85.41528 88.00411 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 163098 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21834 grid for indexing accessible points = 1.400000 m= 80178 mr = 119430 m= 25893 mr = 65822 m= 5500 mr = 20595 m= 641 mr = 4033 m= 37 mr = 399 m= 0 mr = 13 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 21093 time to turn everything in is 0.9100000 number of dielectric boundary points 65055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 19837 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) : 1.837261 object centre at (A) : -7.246000 0.2879992 16.49900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6396634E-02 0.3737687 midg,1,midg; midg,igrid,midg 0.1764608 -9.2087127E-03 1,midg,midg; igrid,midg,midg -5.9027564E-02 0.3545597 gauss-seidel spectral radius is 0.9992251 estimated iterations to convergence 284 setup time was (sec) 1.170000 now iterating at: 11:28:52 rms-change max change #iterations 9.414729 349.7365 at 10iterations 5.386506 141.2610 at 20iterations 3.058698 68.50458 at 30iterations 1.743091 41.85450 at 40iterations 0.9899605 21.70618 at 50iterations 0.5625944 10.56587 at 60iterations 0.3188746 6.353991 at 70iterations 0.1811360 3.439387 at 80iterations 0.1026208 2.075375 at 90iterations 5.8193054E-02 1.176216 at 100iterations 3.2964796E-02 0.6310608 at 110iterations 1.8689236E-02 0.3845654 at 120iterations 1.0606344E-02 0.2344264 at 130iterations 6.0044755E-03 0.1124506 at 140iterations 3.3990173E-03 6.6757202E-02 at 150iterations 1.9293269E-03 3.6067963E-02 at 160iterations 1.0943222E-03 2.0095825E-02 at 170iterations 6.2169175E-04 1.1868477E-02 at 180iterations finished qdiffx linear iterations at : 11:29:10 total time elapsed so far: 14.78000 # loops : 180 mean,max change (kT/e) : 6.2169175E-04 1.1868477E-02 energy calculations done at 14.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.91000 DelPhi exited at 11:29:11 14.914u 0.276s 0:19.92 76.2% 0+0k 0+0io 0pf+0w