Sun Oct 9 12:53:21 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 Sun Oct 9 2011 at 12:53:21 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2412 !!! WARNING: GLM 234 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6927957 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): -5.953000 43.69300 ymin,ymax (A): -14.69800 36.68800 zmin,zma (A): 1.827000 44.32700 x,y,z range (A): 49.64600 51.38600 42.50000 scale (grids/A): 0.6927957 object centre (A): 18.87000 10.99500 23.07700 number of atom coordinates read : 2412 total number of charged atoms : 2266 net assigned charge : 2.406021 assigned positive charge : 369.1439 centred at (gu) : 89.35717 90.74936 90.43734 assigned negative charge : -366.7384 centred at (gu) : 89.37064 90.94646 90.52259 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7691 nv = 96 ne = 84 npr = 48948 no. pairs analyzed = 48948 no. exposed pairs = 2996 no. arc points = 20808 no. surface atoms = 1001 nbur = 1411 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 495 mr = 4245 m= 5 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2200000 number of dielectric boundary points 3876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1939 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8777 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6119069E-08 -2.2592632E-08 midg,1,midg; midg,igrid,midg 8.2192422E-08 -7.9963733E-08 1,midg,midg; igrid,midg,midg 2.3560762E-08 8.4910736E-09 gauss-seidel spectral radius is 0.9891762 estimated iterations to convergence 78 setup time was (sec) 0.4300000 now iterating at: 12:53:21 rms-change max change #iterations 0.2032703 31.77368 at 10iterations 2.3931883E-02 3.076660 at 20iterations 3.0646569E-03 0.3977585 at 30iterations 5.0751370E-04 7.9549789E-02 at 40iterations 1.2171990E-04 2.1415710E-02 at 50iterations finished qdiffx linear iterations at : 12:53:25 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 1.2171990E-04 2.1415710E-02 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 12:53:26 3.659u 0.281s 0:04.91 80.0% 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 12:53:26 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2412 !!! WARNING: GLM 234 has a net charge of -0.0940 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: 2.078387 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): -5.953000 43.69300 ymin,ymax (A): -14.69800 36.68800 zmin,zma (A): 1.827000 44.32700 x,y,z range (A): 49.64600 51.38600 42.50000 scale (grids/A): 2.078387 object centre (A): 18.87000 10.99500 23.07700 number of atom coordinates read : 2412 total number of charged atoms : 2266 net assigned charge : 2.406021 assigned positive charge : 369.1439 centred at (gu) : 88.07092 92.24764 91.31147 assigned negative charge : -366.7384 centred at (gu) : 88.11154 92.83911 91.56753 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20808 grid for indexing accessible points = 1.400000 m= 31961 mr = 56193 m= 6189 mr = 23873 m= 527 mr = 3955 m= 12 mr = 232 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 271 time to turn everything in is 0.4200000 number of dielectric boundary points 35614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 17971 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) : 0.6927957 object centre at (A) : 18.87000 10.99500 23.07700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4055857E-02 -4.9710395E-03 midg,1,midg; midg,igrid,midg 2.5275253E-02 -7.0439912E-02 1,midg,midg; igrid,midg,midg 5.7948992E-02 -1.4297584E-04 gauss-seidel spectral radius is 0.9988259 estimated iterations to convergence 231 setup time was (sec) 0.6700000 now iterating at: 12:53:27 rms-change max change #iterations 4.890720 192.7283 at 10iterations 2.409704 88.16061 at 20iterations 1.192680 37.80672 at 30iterations 0.5868898 17.78781 at 40iterations 0.2904265 8.775783 at 50iterations 0.1436862 4.565602 at 60iterations 7.1202047E-02 2.012835 at 70iterations 3.5324849E-02 1.049160 at 80iterations 1.7559644E-02 0.5315056 at 90iterations 8.7630590E-03 0.2663574 at 100iterations 4.4087609E-03 0.1423621 at 110iterations 2.2424632E-03 6.3503265E-02 at 120iterations finished qdiffx linear iterations at : 12:53:35 total time elapsed so far: 8.120000 # loops : 120 mean,max change (kT/e) : 2.2424632E-03 6.3503265E-02 energy calculations done at 8.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.260000 DelPhi exited at 12:53:35 8.258u 0.842s 0:09.65 94.1% 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 Sun Oct 9 2011 at 12:53:35 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2412 !!! WARNING: GLM 234 has a net charge of -0.0940 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: 3.117581 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): -5.953000 43.69300 ymin,ymax (A): -14.69800 36.68800 zmin,zma (A): 1.827000 44.32700 x,y,z range (A): 49.64600 51.38600 42.50000 scale (grids/A): 3.117581 object centre (A): 18.87000 10.99500 23.07700 number of atom coordinates read : 2412 total number of charged atoms : 2266 net assigned charge : 2.406021 assigned positive charge : 369.1439 centred at (gu) : 87.10614 93.37138 91.96707 assigned negative charge : -366.7384 centred at (gu) : 87.16718 94.25861 92.35125 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 186880 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20808 grid for indexing accessible points = 1.400000 m= 99202 mr = 135631 m= 40669 mr = 81492 m= 11623 mr = 32834 m= 2148 mr = 8828 m= 224 mr = 1475 m= 4 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 975 time to turn everything in is 1.300000 number of dielectric boundary points 80385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 18128 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) : 2.078387 object centre at (A) : 18.87000 10.99500 23.07700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4189250 -0.1465067 midg,1,midg; midg,igrid,midg 0.6107178 -0.7959446 1,midg,midg; igrid,midg,midg 0.9234906 -0.1704177 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 1.530000 now iterating at: 12:53:38 rms-change max change #iterations 11.01981 413.1005 at 10iterations 6.518195 130.8125 at 20iterations 3.856294 77.26105 at 30iterations 2.274719 44.38528 at 40iterations 1.337343 23.93567 at 50iterations 0.7876233 14.45539 at 60iterations 0.4625739 7.895060 at 70iterations 0.2711990 4.455506 at 80iterations 0.1587707 3.123797 at 90iterations 9.3057334E-02 1.466772 at 100iterations 5.4629445E-02 0.9564972 at 110iterations 3.2112319E-02 0.5521393 at 120iterations 1.8959394E-02 0.3241868 at 130iterations 1.1288430E-02 0.1933732 at 140iterations 6.7923493E-03 0.1230888 at 150iterations 4.2127720E-03 8.9176178E-02 at 160iterations 2.7034027E-03 5.4224014E-02 at 170iterations 1.8324143E-03 4.0412903E-02 at 180iterations finished qdiffx linear iterations at : 12:53:49 total time elapsed so far: 13.30000 # loops : 180 mean,max change (kT/e) : 1.8324143E-03 4.0412903E-02 energy calculations done at 13.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.42000 DelPhi exited at 12:53:50 13.419u 0.296s 0:14.35 95.4% 0+0k 0+0io 0pf+0w