Tue Oct 11 07:36:24 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 07:36:24 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2616 !!! WARNING: SEP 202 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6960195 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): -13.30200 37.84600 ymin,ymax (A): -21.68200 26.56500 zmin,zma (A): -5.753000 40.15200 x,y,z range (A): 51.14799 48.24700 45.90500 scale (grids/A): 0.6960195 object centre (A): 12.27200 2.441500 17.19950 number of atom coordinates read : 2616 total number of charged atoms : 2275 net assigned charge : 6.025004 assigned positive charge : 363.5313 centred at (gu) : 90.99663 88.03573 89.51472 assigned negative charge : -357.5067 centred at (gu) : 91.07732 88.01928 89.69141 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7962 nv = 96 ne = 84 npr = 48564 no. pairs analyzed = 48564 no. exposed pairs = 2836 no. arc points = 19590 no. surface atoms = 964 nbur = 1652 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 544 mr = 4699 m= 5 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1753 ## 163 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8893 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2575265E-07 -3.5686817E-08 midg,1,midg; midg,igrid,midg 4.5772147E-08 3.1515714E-08 1,midg,midg; igrid,midg,midg 6.0494990E-08 3.4481704E-09 gauss-seidel spectral radius is 0.9892738 estimated iterations to convergence 79 setup time was (sec) 0.6700000 now iterating at: 07:36:25 rms-change max change #iterations 0.2052019 25.58474 at 10iterations 2.4906838E-02 3.190280 at 20iterations 3.2931825E-03 0.3763008 at 30iterations 5.1557284E-04 7.4104309E-02 at 40iterations 1.0102489E-04 1.4064789E-02 at 50iterations finished qdiffx linear iterations at : 07:36:28 total time elapsed so far: 4.080000 # loops : 50 mean,max change (kT/e) : 1.0102489E-04 1.4064789E-02 energy calculations done at 4.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 07:36:29 4.318u 0.247s 0:04.85 93.8% 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 07:36:29 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2616 !!! WARNING: SEP 202 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.088058 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): -13.30200 37.84600 ymin,ymax (A): -21.68200 26.56500 zmin,zma (A): -5.753000 40.15200 x,y,z range (A): 51.14799 48.24700 45.90500 scale (grids/A): 2.088058 object centre (A): 12.27200 2.441500 17.19950 number of atom coordinates read : 2616 total number of charged atoms : 2275 net assigned charge : 6.025004 assigned positive charge : 363.5313 centred at (gu) : 92.98956 84.10688 88.54382 assigned negative charge : -357.5067 centred at (gu) : 93.23178 84.05755 89.07394 start vw surface at 0.1900000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 83890 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19590 grid for indexing accessible points = 1.400000 m= 34684 mr = 60114 m= 6956 mr = 27013 m= 603 mr = 4713 m= 8 mr = 294 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 34007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 18053 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) : 0.6960195 object centre at (A) : 12.27200 2.441500 17.19950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2985716E-02 -1.2832940E-02 midg,1,midg; midg,igrid,midg 1.5622983E-02 2.4319034E-02 1,midg,midg; igrid,midg,midg 1.8729951E-02 1.9984070E-02 gauss-seidel spectral radius is 0.9988257 estimated iterations to convergence 231 setup time was (sec) 1.180000 now iterating at: 07:36:30 rms-change max change #iterations 4.857499 229.1892 at 10iterations 2.411883 84.43549 at 20iterations 1.192323 34.74795 at 30iterations 0.5925503 18.35452 at 40iterations 0.2945506 8.526919 at 50iterations 0.1464269 4.794353 at 60iterations 7.2707266E-02 2.028993 at 70iterations 3.6175590E-02 0.9949436 at 80iterations 1.8002423E-02 0.4857063 at 90iterations 8.9785811E-03 0.2482910 at 100iterations 4.4958834E-03 0.1359262 at 110iterations 2.2715728E-03 7.5859070E-02 at 120iterations finished qdiffx linear iterations at : 07:36:38 total time elapsed so far: 9.600000 # loops : 120 mean,max change (kT/e) : 2.2715728E-03 7.5859070E-02 energy calculations done at 9.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.830000 DelPhi exited at 07:36:39 9.832u 0.264s 0:10.42 96.8% 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 07:36:39 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2616 !!! WARNING: SEP 202 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 3.132087 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): -13.30200 37.84600 ymin,ymax (A): -21.68200 26.56500 zmin,zma (A): -5.753000 40.15200 x,y,z range (A): 51.14799 48.24700 45.90500 scale (grids/A): 3.132087 object centre (A): 12.27200 2.441500 17.19950 number of atom coordinates read : 2616 total number of charged atoms : 2275 net assigned charge : 6.025004 assigned positive charge : 363.5313 centred at (gu) : 94.48411 81.16026 87.81570 assigned negative charge : -357.5067 centred at (gu) : 94.84760 81.08631 88.61089 start vw surface at 0.2000000 fill in re-entrant regions at 1.150000 boundary points on vw surface= 193548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19590 grid for indexing accessible points = 1.400000 m= 106900 mr = 144568 m= 45256 mr = 90243 m= 13031 mr = 37777 m= 2511 mr = 10199 m= 242 mr = 1835 m= 3 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 1.270000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.570000 number of dielectric boundary points 76731 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.730000 number of grid points assigned charge 18200 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) : 2.088058 object centre at (A) : 12.27200 2.441500 17.19950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5130478 -0.1467844 midg,1,midg; midg,igrid,midg 0.1029430 0.1610616 1,midg,midg; igrid,midg,midg 1.9477274E-02 4.7930591E-02 gauss-seidel spectral radius is 0.9993005 estimated iterations to convergence 298 setup time was (sec) 2.960000 now iterating at: 07:36:42 rms-change max change #iterations 10.79380 414.2321 at 10iterations 6.346238 153.5958 at 20iterations 3.738356 68.91028 at 30iterations 2.191672 34.54829 at 40iterations 1.284943 19.48177 at 50iterations 0.7504845 12.09855 at 60iterations 0.4392175 7.346704 at 70iterations 0.2568828 4.022510 at 80iterations 0.1503573 2.428844 at 90iterations 8.8072278E-02 1.513657 at 100iterations 5.1662922E-02 0.8783078 at 110iterations 3.0390609E-02 0.5121994 at 120iterations 1.8007960E-02 0.3482399 at 130iterations 1.0761414E-02 0.1977272 at 140iterations 6.5298895E-03 0.1131210 at 150iterations 4.0914128E-03 7.2471619E-02 at 160iterations 2.6659998E-03 5.1643372E-02 at 170iterations 1.8172942E-03 3.2783508E-02 at 180iterations finished qdiffx linear iterations at : 07:36:56 total time elapsed so far: 16.46000 # loops : 180 mean,max change (kT/e) : 1.8172942E-03 3.2783508E-02 energy calculations done at 16.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.70000 DelPhi exited at 07:36:56 16.697u 0.306s 0:17.38 97.7% 0+0k 0+0io 0pf+0w