Sat Oct 8 19:39:46 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 19:39:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: GLM 1092 has a net charge of -0.0940 !!! WARNING: HIR 1094 has a net charge of 0.5140 !!! WARNING: HIR 1096 has a net charge of 0.5140 !!! WARNING: HIR 1119 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: 0.6193781 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): -10.31800 38.77700 ymin,ymax (A): -22.47300 24.94900 zmin,zma (A): -12.43100 45.04600 x,y,z range (A): 49.09500 47.42200 57.47700 scale (grids/A): 0.6193781 object centre (A): 14.22950 1.238000 16.30750 number of atom coordinates read : 2565 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 392.9700 centred at (gu) : 88.50739 89.30400 89.68359 assigned negative charge : -389.5226 centred at (gu) : 88.40886 89.37530 89.56478 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6415 nv = 96 ne = 84 npr = 52688 no. pairs analyzed = 52688 no. exposed pairs = 2953 no. arc points = 21373 no. surface atoms = 1001 nbur = 1564 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 307 mr = 3556 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 131 time to turn everything in is 0.2800000 number of dielectric boundary points 3129 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2145 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8008 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4235807E-09 9.7746531E-09 midg,1,midg; midg,igrid,midg 8.6853094E-09 -1.5802155E-09 1,midg,midg; igrid,midg,midg -5.2361897E-09 6.6257035E-09 gauss-seidel spectral radius is 0.9864956 estimated iterations to convergence 70 setup time was (sec) 0.5200000 now iterating at: 19:39:46 rms-change max change #iterations 0.1252975 19.40233 at 10iterations 1.1593095E-02 1.789660 at 20iterations 1.0949754E-03 0.1794634 at 30iterations 1.0119472E-04 1.3526917E-02 at 40iterations 9.8599912E-06 1.4803410E-03 at 50iterations finished qdiffx linear iterations at : 19:39:49 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 9.8599912E-06 1.4803410E-03 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 19:39:49 3.278u 0.168s 0:03.72 92.2% 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 19:39:50 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: GLM 1092 has a net charge of -0.0940 !!! WARNING: HIR 1094 has a net charge of 0.5140 !!! WARNING: HIR 1096 has a net charge of 0.5140 !!! WARNING: HIR 1119 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.858135 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): -10.31800 38.77700 ymin,ymax (A): -22.47300 24.94900 zmin,zma (A): -12.43100 45.04600 x,y,z range (A): 49.09500 47.42200 57.47700 scale (grids/A): 1.858135 object centre (A): 14.22950 1.238000 16.30750 number of atom coordinates read : 2565 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 392.9700 centred at (gu) : 85.52194 87.91130 89.05037 assigned negative charge : -389.5226 centred at (gu) : 85.22648 88.12556 88.69448 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21373 grid for indexing accessible points = 1.400000 m= 24228 mr = 49073 m= 3354 mr = 17949 m= 181 mr = 2028 m= 4 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 5031 time to turn everything in is 0.4900000 number of dielectric boundary points 28888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19193 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) : 0.6193781 object centre at (A) : 14.22950 1.238000 16.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8259805E-02 3.3687826E-02 midg,1,midg; midg,igrid,midg 1.4247330E-02 2.9323359E-03 1,midg,midg; igrid,midg,midg -8.7030521E-03 2.8562604E-02 gauss-seidel spectral radius is 0.9985633 estimated iterations to convergence 209 setup time was (sec) 0.7900000 now iterating at: 19:39:50 rms-change max change #iterations 4.022833 182.1732 at 10iterations 1.844652 71.31815 at 20iterations 0.8493419 29.85070 at 30iterations 0.3888561 13.67897 at 40iterations 0.1793415 6.705440 at 50iterations 8.2121283E-02 2.446859 at 60iterations 3.7783619E-02 1.197510 at 70iterations 1.7302638E-02 0.5407342 at 80iterations 7.9584867E-03 0.2656593 at 90iterations 3.6707167E-03 0.1242914 at 100iterations 1.6857537E-03 5.3858757E-02 at 110iterations 7.7661412E-04 2.6806355E-02 at 120iterations finished qdiffx linear iterations at : 19:39:57 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 7.7661412E-04 2.6806355E-02 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.340000 DelPhi exited at 19:39:57 7.338u 0.192s 0:07.80 96.4% 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 8 2011 at 19:39:57 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2565 !!! WARNING: GLM 1092 has a net charge of -0.0940 !!! WARNING: HIR 1094 has a net charge of 0.5140 !!! WARNING: HIR 1096 has a net charge of 0.5140 !!! WARNING: HIR 1119 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.787202 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): -10.31800 38.77700 ymin,ymax (A): -22.47300 24.94900 zmin,zma (A): -12.43100 45.04600 x,y,z range (A): 49.09500 47.42200 57.47700 scale (grids/A): 2.787202 object centre (A): 14.22950 1.238000 16.30750 number of atom coordinates read : 2565 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 392.9700 centred at (gu) : 83.28268 86.86691 88.57552 assigned negative charge : -389.5226 centred at (gu) : 82.83970 87.18821 88.04166 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 162358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21373 grid for indexing accessible points = 1.400000 m= 80443 mr = 118453 m= 27332 mr = 66461 m= 6020 mr = 21878 m= 760 mr = 4470 m= 38 mr = 477 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 17340 time to turn everything in is 1.250000 number of dielectric boundary points 65193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 19591 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) : 1.858135 object centre at (A) : 14.22950 1.238000 16.30750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.4352123E-02 0.5005623 midg,1,midg; midg,igrid,midg 0.1621821 1.9952575E-02 1,midg,midg; igrid,midg,midg -6.5175623E-02 0.3940293 gauss-seidel spectral radius is 0.9992329 estimated iterations to convergence 285 setup time was (sec) 1.560000 now iterating at: 19:39:59 rms-change max change #iterations 9.478305 343.5243 at 10iterations 5.450094 127.5891 at 20iterations 3.116096 65.82762 at 30iterations 1.776076 37.18897 at 40iterations 1.010515 19.83965 at 50iterations 0.5751091 11.65407 at 60iterations 0.3275389 6.548222 at 70iterations 0.1859439 3.605074 at 80iterations 0.1058308 2.015611 at 90iterations 6.0180981E-02 1.162697 at 100iterations 3.4204751E-02 0.7100821 at 110iterations 1.9482791E-02 0.3930817 at 120iterations 1.1077606E-02 0.2016659 at 130iterations 6.2944489E-03 0.1194916 at 140iterations 3.5804131E-03 7.0173264E-02 at 150iterations 2.0384716E-03 3.8202286E-02 at 160iterations 1.1595265E-03 2.1018982E-02 at 170iterations 6.6406548E-04 1.2239456E-02 at 180iterations finished qdiffx linear iterations at : 19:40:11 total time elapsed so far: 13.25000 # loops : 180 mean,max change (kT/e) : 6.6406548E-04 1.2239456E-02 energy calculations done at 13.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.43000 DelPhi exited at 19:40:11 13.429u 0.217s 0:13.93 97.8% 0+0k 0+0io 0pf+0w