Tue Oct 11 05:49:51 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 05:49:51 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2034 !!! WARNING: SEP 190 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7080632 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): -20.18000 23.80600 ymin,ymax (A): -11.97000 28.73700 zmin,zma (A): -3.482000 46.79600 x,y,z range (A): 43.98600 40.70700 50.27800 scale (grids/A): 0.7080632 object centre (A): 1.813000 8.383500 21.65700 number of atom coordinates read : 2034 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 312.5171 centred at (gu) : 90.16651 89.69793 90.46639 assigned negative charge : -305.4922 centred at (gu) : 89.98164 89.71932 90.48528 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6939 nv = 96 ne = 84 npr = 40493 no. pairs analyzed = 40493 no. exposed pairs = 2443 no. arc points = 16681 no. surface atoms = 838 nbur = 1196 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 454 mr = 4000 m= 4 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 3327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1635 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7773 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3499137E-08 5.5403014E-08 midg,1,midg; midg,igrid,midg 7.4736356E-08 4.6869793E-08 1,midg,midg; igrid,midg,midg -3.1217020E-08 1.5414147E-07 gauss-seidel spectral radius is 0.9895973 estimated iterations to convergence 80 setup time was (sec) 0.3500000 now iterating at: 05:49:52 rms-change max change #iterations 0.2048200 29.39320 at 10iterations 2.5433643E-02 3.385104 at 20iterations 3.3878300E-03 0.4562531 at 30iterations 5.5810227E-04 7.2052956E-02 at 40iterations 1.3072896E-04 1.7074585E-02 at 50iterations finished qdiffx linear iterations at : 05:49:55 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.3072896E-04 1.7074585E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 05:49:55 3.360u 0.175s 0:03.83 92.1% 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 Tue Oct 11 2011 at 05:49:55 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2034 !!! WARNING: SEP 190 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.124190 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): -20.18000 23.80600 ymin,ymax (A): -11.97000 28.73700 zmin,zma (A): -3.482000 46.79600 x,y,z range (A): 43.98600 40.70700 50.27800 scale (grids/A): 2.124190 object centre (A): 1.813000 8.383500 21.65700 number of atom coordinates read : 2034 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 312.5171 centred at (gu) : 90.49953 89.09399 91.39919 assigned negative charge : -305.4922 centred at (gu) : 89.94500 89.15802 91.45612 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16681 grid for indexing accessible points = 1.400000 m= 29457 mr = 52333 m= 5884 mr = 22353 m= 567 mr = 3959 m= 19 mr = 313 m= 0 mr = 4 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 30513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 15302 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) : 0.7080632 object centre at (A) : 1.813000 8.383500 21.65700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0786477E-02 6.7396171E-02 midg,1,midg; midg,igrid,midg 3.0448183E-02 4.9803425E-03 1,midg,midg; igrid,midg,midg 1.2088272E-02 4.3408498E-02 gauss-seidel spectral radius is 0.9988278 estimated iterations to convergence 231 setup time was (sec) 0.5900000 now iterating at: 05:49:56 rms-change max change #iterations 4.609890 240.7240 at 10iterations 2.278559 80.32544 at 20iterations 1.130645 35.51635 at 30iterations 0.5590871 17.43433 at 40iterations 0.2784972 8.700852 at 50iterations 0.1384200 4.356457 at 60iterations 6.8793871E-02 2.173639 at 70iterations 3.4160938E-02 1.020365 at 80iterations 1.6986275E-02 0.5319901 at 90iterations 8.4889503E-03 0.2479591 at 100iterations 4.2606299E-03 0.1366625 at 110iterations 2.1577803E-03 6.8845272E-02 at 120iterations finished qdiffx linear iterations at : 05:50:03 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 2.1577803E-03 6.8845272E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 05:50:04 7.815u 0.194s 0:08.49 94.2% 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 Tue Oct 11 2011 at 05:50:04 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2034 !!! WARNING: SEP 190 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.186284 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): -20.18000 23.80600 ymin,ymax (A): -11.97000 28.73700 zmin,zma (A): -3.482000 46.79600 x,y,z range (A): 43.98600 40.70700 50.27800 scale (grids/A): 3.186284 object centre (A): 1.813000 8.383500 21.65700 number of atom coordinates read : 2034 total number of charged atoms : 1927 net assigned charge : 7.025010 assigned positive charge : 312.5171 centred at (gu) : 90.74928 88.64092 92.09878 assigned negative charge : -305.4922 centred at (gu) : 89.91746 88.73707 92.18405 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 169753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16681 grid for indexing accessible points = 1.400000 m= 92022 mr = 126242 m= 37600 mr = 76646 m= 11085 mr = 30974 m= 2268 mr = 8580 m= 270 mr = 1702 m= 9 mr = 181 m= 0 mr = 3 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 68679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 15416 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) : 2.124190 object centre at (A) : 1.813000 8.383500 21.65700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2399435 0.7044868 midg,1,midg; midg,igrid,midg 0.2402920 1.1799335E-03 1,midg,midg; igrid,midg,midg 0.2257020 0.3023323 gauss-seidel spectral radius is 0.9992928 estimated iterations to convergence 297 setup time was (sec) 1.390000 now iterating at: 05:50:05 rms-change max change #iterations 10.19548 296.1058 at 10iterations 6.012099 151.9356 at 20iterations 3.539242 76.45516 at 30iterations 2.085104 40.00117 at 40iterations 1.227429 22.54794 at 50iterations 0.7206082 15.48394 at 60iterations 0.4226179 8.035874 at 70iterations 0.2475664 4.341858 at 80iterations 0.1451031 2.768131 at 90iterations 8.4679842E-02 1.508995 at 100iterations 4.9772531E-02 0.9144592 at 110iterations 2.9354729E-02 0.5516815 at 120iterations 1.7401701E-02 0.3234148 at 130iterations 1.0473633E-02 0.1919785 at 140iterations 6.4434274E-03 0.1278381 at 150iterations 4.0894961E-03 7.9833984E-02 at 160iterations 2.7372679E-03 5.9066772E-02 at 170iterations 1.9315542E-03 3.9245605E-02 at 180iterations finished qdiffx linear iterations at : 05:50:17 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 1.9315542E-03 3.9245605E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.83000 DelPhi exited at 05:50:17 12.835u 0.194s 0:13.71 94.9% 0+0k 0+0io 0pf+0w