Sun Oct 9 13:30:01 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+sph.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 = amb.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 Sun Oct 9 2011 at 13:30:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2375 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6755987 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): -6.819000 44.60800 ymin,ymax (A): -14.19500 38.49900 zmin,zma (A): 1.418000 44.54900 x,y,z range (A): 51.42700 52.69400 43.13100 scale (grids/A): 0.6755987 object centre (A): 18.89450 12.15200 22.98350 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500019 assigned positive charge : 361.0370 centred at (gu) : 89.61884 90.78223 91.02784 assigned negative charge : -357.5376 centred at (gu) : 89.60884 90.94094 91.07270 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7340 nv = 96 ne = 84 npr = 47503 no. pairs analyzed = 47503 no. exposed pairs = 3034 no. arc points = 21315 no. surface atoms = 1014 nbur = 1361 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 394 mr = 3983 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2066 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8470 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1145807E-08 2.1113973E-09 midg,1,midg; midg,igrid,midg 4.7698634E-08 -3.4772167E-08 1,midg,midg; igrid,midg,midg 1.2164172E-08 1.5456726E-08 gauss-seidel spectral radius is 0.9886216 estimated iterations to convergence 76 setup time was (sec) 0.4900000 now iterating at: 13:30:02 rms-change max change #iterations 0.1719657 25.66041 at 10iterations 1.9497555E-02 3.211649 at 20iterations 2.7362336E-03 0.4303284 at 30iterations 6.3558522E-04 0.1047974 at 40iterations 2.0876386E-04 3.4656525E-02 at 50iterations finished qdiffx linear iterations at : 13:30:04 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 2.0876386E-04 3.4656525E-02 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 13:30:05 3.135u 0.142s 0:03.54 92.3% 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 Sun Oct 9 2011 at 13:30:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2375 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: 2.026796 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): -6.819000 44.60800 ymin,ymax (A): -14.19500 38.49900 zmin,zma (A): 1.418000 44.54900 x,y,z range (A): 51.42700 52.69400 43.13100 scale (grids/A): 2.026796 object centre (A): 18.89450 12.15200 22.98350 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500019 assigned positive charge : 361.0370 centred at (gu) : 88.85593 92.34605 93.08305 assigned negative charge : -357.5376 centred at (gu) : 88.82621 92.82263 93.21800 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 78505 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21315 grid for indexing accessible points = 1.400000 m= 29219 mr = 54321 m= 4805 mr = 21378 m= 367 mr = 2925 m= 6 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 34111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 17671 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) : 0.6755987 object centre at (A) : 18.89450 12.15200 22.98350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3776604E-02 1.0458521E-02 midg,1,midg; midg,igrid,midg 1.5901595E-02 -4.6817549E-02 1,midg,midg; igrid,midg,midg 3.9986756E-02 -8.1287343E-03 gauss-seidel spectral radius is 0.9987707 estimated iterations to convergence 226 setup time was (sec) 0.8100000 now iterating at: 13:30:06 rms-change max change #iterations 4.602422 200.7603 at 10iterations 2.226633 82.18216 at 20iterations 1.083303 33.31134 at 30iterations 0.5270930 16.91403 at 40iterations 0.2568765 7.663894 at 50iterations 0.1252881 4.169800 at 60iterations 6.1335292E-02 1.991737 at 70iterations 2.9861450E-02 0.8945160 at 80iterations 1.4706697E-02 0.4431000 at 90iterations 7.3467838E-03 0.2268815 at 100iterations 3.7351712E-03 0.1127129 at 110iterations 1.9696865E-03 6.3142300E-02 at 120iterations finished qdiffx linear iterations at : 13:30:12 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 1.9696865E-03 6.3142300E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 13:30:13 7.153u 0.145s 0:07.57 96.3% 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 Sun Oct 9 2011 at 13:30:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2375 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 3.040194 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): -6.819000 44.60800 ymin,ymax (A): -14.19500 38.49900 zmin,zma (A): 1.418000 44.54900 x,y,z range (A): 51.42700 52.69400 43.13100 scale (grids/A): 3.040194 object centre (A): 18.89450 12.15200 22.98350 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500019 assigned positive charge : 361.0370 centred at (gu) : 88.28381 93.51900 94.62452 assigned negative charge : -357.5376 centred at (gu) : 88.23937 94.23397 94.82696 start vw surface at 0.2000000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 181389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21315 grid for indexing accessible points = 1.400000 m= 93738 mr = 131646 m= 34479 mr = 76450 m= 8529 mr = 27405 m= 1472 mr = 6289 m= 162 mr = 999 m= 5 mr = 97 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.510000 number of dielectric boundary points 76888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 17871 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) : 2.026796 object centre at (A) : 18.89450 12.15200 22.98350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3625828 -1.5977258E-02 midg,1,midg; midg,igrid,midg 0.2970437 -0.6307324 1,midg,midg; igrid,midg,midg 0.5049709 -0.3160782 gauss-seidel spectral radius is 0.9992853 estimated iterations to convergence 295 setup time was (sec) 1.790000 now iterating at: 13:30:15 rms-change max change #iterations 10.50986 426.4698 at 10iterations 6.212327 119.4188 at 20iterations 3.677089 80.29237 at 30iterations 2.165484 44.21890 at 40iterations 1.271787 22.32390 at 50iterations 0.7449844 14.15644 at 60iterations 0.4361643 7.763820 at 70iterations 0.2547186 4.474495 at 80iterations 0.1491119 2.954447 at 90iterations 8.7081999E-02 1.542951 at 100iterations 5.1022340E-02 0.9592991 at 110iterations 2.9901167E-02 0.5479298 at 120iterations 1.7689083E-02 0.3454437 at 130iterations 1.0642158E-02 0.2031059 at 140iterations 6.5649371E-03 0.1231689 at 150iterations 4.2321831E-03 8.6811066E-02 at 160iterations 2.8915908E-03 6.6337585E-02 at 170iterations 2.1065478E-03 5.4641724E-02 at 180iterations finished qdiffx linear iterations at : 13:30:24 total time elapsed so far: 11.16000 # loops : 180 mean,max change (kT/e) : 2.1065478E-03 5.4641724E-02 energy calculations done at 11.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.36000 DelPhi exited at 13:30:24 11.362u 0.175s 0:11.79 97.7% 0+0k 0+0io 0pf+0w