Tue Oct 11 06:00:23 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 Tue Oct 11 2011 at 06:00:23 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 0.7086692 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): 25.68600 72.53800 ymin,ymax (A): -18.66800 31.56700 zmin,zma (A): 4.031000 46.32200 x,y,z range (A): 46.85201 50.23500 42.29100 scale (grids/A): 0.7086692 object centre (A): 49.11200 6.449500 25.17650 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 89.09604 90.17169 90.29307 assigned negative charge : -317.2741 centred at (gu) : 89.22469 90.12492 90.37704 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7174 nv = 96 ne = 84 npr = 42905 no. pairs analyzed = 42905 no. exposed pairs = 2587 no. arc points = 17374 no. surface atoms = 887 nbur = 1431 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 464 mr = 4131 m= 3 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3423 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1654 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8046 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3519624E-08 1.2684124E-08 midg,1,midg; midg,igrid,midg 3.0680557E-08 8.2639673E-08 1,midg,midg; igrid,midg,midg 1.4495946E-07 -9.0264010E-09 gauss-seidel spectral radius is 0.9896216 estimated iterations to convergence 80 setup time was (sec) 0.4900000 now iterating at: 06:00:23 rms-change max change #iterations 0.2033598 34.43657 at 10iterations 2.5505751E-02 4.064955 at 20iterations 3.3405097E-03 0.4121284 at 30iterations 5.5478362E-04 8.0459595E-02 at 40iterations 1.3599492E-04 1.6975403E-02 at 50iterations finished qdiffx linear iterations at : 06:00:26 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 1.3599492E-04 1.6975403E-02 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 06:00:27 3.250u 0.183s 0:03.97 86.3% 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 Tue Oct 11 2011 at 06:00:27 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 2.126008 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): 25.68600 72.53800 ymin,ymax (A): -18.66800 31.56700 zmin,zma (A): 4.031000 46.32200 x,y,z range (A): 46.85201 50.23500 42.29100 scale (grids/A): 2.126008 object centre (A): 49.11200 6.449500 25.17650 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 87.28794 90.51516 90.87903 assigned negative charge : -317.2741 centred at (gu) : 87.67423 90.37480 91.13133 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 76026 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17374 grid for indexing accessible points = 1.400000 m= 30945 mr = 54268 m= 6076 mr = 23665 m= 584 mr = 4080 m= 22 mr = 295 m= 0 mr = 4 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 31341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 15819 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) : 0.7086692 object centre at (A) : 49.11200 6.449500 25.17650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3173464E-02 2.9450335E-02 midg,1,midg; midg,igrid,midg 4.7722228E-02 2.9654870E-02 1,midg,midg; igrid,midg,midg 4.3970037E-02 -4.3058660E-02 gauss-seidel spectral radius is 0.9988362 estimated iterations to convergence 232 setup time was (sec) 0.8400000 now iterating at: 06:00:28 rms-change max change #iterations 4.641203 183.6304 at 10iterations 2.297948 75.07795 at 20iterations 1.140436 39.83446 at 30iterations 0.5676390 16.39534 at 40iterations 0.2831571 8.676449 at 50iterations 0.1405441 4.166090 at 60iterations 6.9864869E-02 1.953101 at 70iterations 3.4893468E-02 1.114567 at 80iterations 1.7359784E-02 0.5522995 at 90iterations 8.7151220E-03 0.2865601 at 100iterations 4.3848646E-03 0.1375710 at 110iterations 2.2549597E-03 6.7550182E-02 at 120iterations finished qdiffx linear iterations at : 06:00:34 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 2.2549597E-03 6.7550182E-02 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.410000 DelPhi exited at 06:00:35 7.412u 0.225s 0:07.90 96.5% 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 06:00:35 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 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: 3.189012 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): 25.68600 72.53800 ymin,ymax (A): -18.66800 31.56700 zmin,zma (A): 4.031000 46.32200 x,y,z range (A): 46.85201 50.23500 42.29100 scale (grids/A): 3.189012 object centre (A): 49.11200 6.449500 25.17650 number of atom coordinates read : 2318 total number of charged atoms : 1994 net assigned charge : 6.500009 assigned positive charge : 323.7739 centred at (gu) : 85.93211 90.77280 91.31852 assigned negative charge : -317.2741 centred at (gu) : 86.51138 90.56217 91.69693 start vw surface at 0.1500000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 175181 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17374 grid for indexing accessible points = 1.400000 m= 96115 mr = 130411 m= 39334 mr = 80199 m= 11442 mr = 32510 m= 2380 mr = 8926 m= 288 mr = 1725 m= 24 mr = 200 m= 0 mr = 8 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.770000 number of dielectric boundary points 70785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 15952 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) : 2.126008 object centre at (A) : 49.11200 6.449500 25.17650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1450053 0.2495875 midg,1,midg; midg,igrid,midg 0.3882973 0.1443971 1,midg,midg; igrid,midg,midg 0.4381100 -0.5242616 gauss-seidel spectral radius is 0.9992971 estimated iterations to convergence 298 setup time was (sec) 2.080000 now iterating at: 06:00:37 rms-change max change #iterations 10.36392 295.9415 at 10iterations 6.120267 125.4673 at 20iterations 3.619216 87.56581 at 30iterations 2.134419 42.77575 at 40iterations 1.253356 24.60947 at 50iterations 0.7391039 13.74778 at 60iterations 0.4334937 7.778320 at 70iterations 0.2542764 4.860352 at 80iterations 0.1490285 2.536221 at 90iterations 8.7396339E-02 1.527573 at 100iterations 5.1338278E-02 0.9878654 at 110iterations 3.0259425E-02 0.5612154 at 120iterations 1.7918492E-02 0.3514640 at 130iterations 1.0762696E-02 0.1885986 at 140iterations 6.5930057E-03 0.1199722 at 150iterations 4.1779773E-03 8.1054688E-02 at 160iterations 2.7812493E-03 5.3813934E-02 at 170iterations 1.9552070E-03 3.8082123E-02 at 180iterations finished qdiffx linear iterations at : 06:00:47 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 1.9552070E-03 3.8082123E-02 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 06:00:48 12.607u 0.213s 0:13.51 94.8% 0+0k 0+0io 0pf+0w