Tue Oct 11 03:48:05 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 03:48:05 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2747 !!! WARNING: TYS 279 has a net charge of -0.6490 !!! WARNING: TYS 1 has a net charge of -0.3380 !!! WARNING: TYS 2 has a net charge of -0.3380 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: 0.6783019 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): 3.675000 56.15900 ymin,ymax (A): 17.84600 69.59299 zmin,zma (A): 20.73000 73.17800 x,y,z range (A): 52.48400 51.74699 52.44800 scale (grids/A): 0.6783019 object centre (A): 29.91700 43.71950 46.95400 number of atom coordinates read : 2747 total number of charged atoms : 2596 net assigned charge : 4.175016 assigned positive charge : 412.2198 centred at (gu) : 89.33700 89.60651 89.38680 assigned negative charge : -408.0455 centred at (gu) : 89.61108 89.63890 89.54713 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8603 nv = 96 ne = 84 npr = 56003 no. pairs analyzed = 56003 no. exposed pairs = 3384 no. arc points = 23588 no. surface atoms = 1139 nbur = 1608 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 504 mr = 4940 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3000000 number of dielectric boundary points 4088 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2243 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9858 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.7178036E-08 -3.2699194E-08 midg,1,midg; midg,igrid,midg 2.9087460E-08 5.2463300E-09 1,midg,midg; igrid,midg,midg 1.1894947E-07 -6.6416611E-08 gauss-seidel spectral radius is 0.9887442 estimated iterations to convergence 77 setup time was (sec) 0.5400000 now iterating at: 03:48:06 rms-change max change #iterations 0.1963293 26.72334 at 10iterations 2.1985840E-02 2.869900 at 20iterations 2.5454850E-03 0.3166065 at 30iterations 3.0210300E-04 3.9339066E-02 at 40iterations 3.8686776E-05 4.6749115E-03 at 50iterations finished qdiffx linear iterations at : 03:48:09 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 3.8686776E-05 4.6749115E-03 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 03:48:09 3.237u 0.166s 0:03.92 86.4% 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 03:48:09 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2747 !!! WARNING: TYS 279 has a net charge of -0.6490 !!! WARNING: TYS 1 has a net charge of -0.3380 !!! WARNING: TYS 2 has a net charge of -0.3380 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: 2.034906 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): 3.675000 56.15900 ymin,ymax (A): 17.84600 69.59299 zmin,zma (A): 20.73000 73.17800 x,y,z range (A): 52.48400 51.74699 52.44800 scale (grids/A): 2.034906 object centre (A): 29.91700 43.71950 46.95400 number of atom coordinates read : 2747 total number of charged atoms : 2596 net assigned charge : 4.175016 assigned positive charge : 412.2198 centred at (gu) : 88.01032 88.81898 88.15977 assigned negative charge : -408.0455 centred at (gu) : 88.83282 88.91636 88.64099 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 91133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23588 grid for indexing accessible points = 1.400000 m= 36685 mr = 64668 m= 6932 mr = 28151 m= 557 mr = 4723 m= 9 mr = 256 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1635 time to turn everything in is 0.6600000 number of dielectric boundary points 37518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20521 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) : 0.6783019 object centre at (A) : 29.91700 43.71950 46.95400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2673747E-02 -2.7823895E-02 midg,1,midg; midg,igrid,midg 3.6902606E-02 -5.2622152E-03 1,midg,midg; igrid,midg,midg 5.0196841E-02 -1.5326916E-02 gauss-seidel spectral radius is 0.9988098 estimated iterations to convergence 229 setup time was (sec) 0.9500000 now iterating at: 03:48:10 rms-change max change #iterations 5.002628 266.2511 at 10iterations 2.453389 83.92130 at 20iterations 1.204553 35.79487 at 30iterations 0.5957071 18.00872 at 40iterations 0.2940763 8.178982 at 50iterations 0.1451495 4.335918 at 60iterations 7.1396425E-02 1.932777 at 70iterations 3.5316397E-02 1.042137 at 80iterations 1.7332457E-02 0.4635439 at 90iterations 8.5623404E-03 0.2950478 at 100iterations 4.2190379E-03 0.1191750 at 110iterations 2.0863907E-03 6.3519478E-02 at 120iterations finished qdiffx linear iterations at : 03:48:17 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 2.0863907E-03 6.3519478E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 03:48:18 7.773u 0.199s 0:08.52 93.4% 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 03:48:18 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2747 !!! WARNING: TYS 279 has a net charge of -0.6490 !!! WARNING: TYS 1 has a net charge of -0.3380 !!! WARNING: TYS 2 has a net charge of -0.3380 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: 3.052359 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): 3.675000 56.15900 ymin,ymax (A): 17.84600 69.59299 zmin,zma (A): 20.73000 73.17800 x,y,z range (A): 52.48400 51.74699 52.44800 scale (grids/A): 3.052359 object centre (A): 29.91700 43.71950 46.95400 number of atom coordinates read : 2747 total number of charged atoms : 2596 net assigned charge : 4.175016 assigned positive charge : 412.2198 centred at (gu) : 87.01546 88.22841 87.23967 assigned negative charge : -408.0455 centred at (gu) : 88.24928 88.37455 87.96139 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 210138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23588 grid for indexing accessible points = 1.400000 m= 114024 mr = 155398 m= 47015 mr = 95490 m= 13168 mr = 39223 m= 2363 mr = 10295 m= 213 mr = 1739 m= 3 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 5179 time to turn everything in is 1.690000 number of dielectric boundary points 84676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 20754 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) : 2.034906 object centre at (A) : 29.91700 43.71950 46.95400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3352015 -0.3809831 midg,1,midg; midg,igrid,midg 0.3133741 -0.1902695 1,midg,midg; igrid,midg,midg 0.1432211 -1.9005764E-02 gauss-seidel spectral radius is 0.9993017 estimated iterations to convergence 299 setup time was (sec) 1.990000 now iterating at: 03:48:20 rms-change max change #iterations 11.14984 509.7606 at 10iterations 6.560793 126.0973 at 20iterations 3.862342 79.37323 at 30iterations 2.269802 39.78584 at 40iterations 1.337285 28.52404 at 50iterations 0.7841823 12.55389 at 60iterations 0.4602228 7.695436 at 70iterations 0.2695158 4.666996 at 80iterations 0.1578272 2.712855 at 90iterations 9.2409067E-02 1.446093 at 100iterations 5.4244198E-02 0.9772277 at 110iterations 3.1719018E-02 0.5159073 at 120iterations 1.8605879E-02 0.3159833 at 130iterations 1.0909577E-02 0.1804161 at 140iterations 6.3907928E-03 0.1055775 at 150iterations 3.7570102E-03 6.2164307E-02 at 160iterations 2.2220830E-03 3.4147263E-02 at 170iterations 1.3217914E-03 2.2075653E-02 at 180iterations finished qdiffx linear iterations at : 03:48:31 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 1.3217914E-03 2.2075653E-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) 12.88000 DelPhi exited at 03:48:31 12.882u 0.237s 0:13.55 96.7% 0+0k 0+0io 0pf+0w