Mon Oct 10 13:59:22 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 Mon Oct 10 2011 at 13:59:22 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5739436 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): -11.10400 50.92300 ymin,ymax (A): -13.23600 42.47000 zmin,zma (A): 19.31800 75.58100 x,y,z range (A): 62.02700 55.70600 56.26300 scale (grids/A): 0.5739436 object centre (A): 19.90950 14.61700 47.44950 number of atom coordinates read : 3366 total number of charged atoms : 3209 net assigned charge : 4.240020 assigned positive charge : 520.1039 centred at (gu) : 90.90414 89.85836 87.80712 assigned negative charge : -515.8651 centred at (gu) : 90.76860 89.94274 87.78566 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7402 nv = 96 ne = 84 npr = 65575 no. pairs analyzed = 65575 no. exposed pairs = 4526 no. arc points = 31439 no. surface atoms = 1506 nbur = 1860 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 367 mr = 3728 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 4020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3109 ## 345 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9294 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4586757E-10 7.0630568E-10 midg,1,midg; midg,igrid,midg 2.5414477E-09 -1.0040452E-09 1,midg,midg; igrid,midg,midg -1.7076799E-09 4.3330890E-09 gauss-seidel spectral radius is 0.9843701 estimated iterations to convergence 66 setup time was (sec) 0.6300000 now iterating at: 13:59:23 rms-change max change #iterations 9.7794302E-02 15.15929 at 10iterations 7.4597481E-03 1.073178 at 20iterations 5.7975145E-04 9.3765259E-02 at 30iterations 4.4686716E-05 6.4558983E-03 at 40iterations 3.9409215E-06 5.7983398E-04 at 50iterations finished qdiffx linear iterations at : 13:59:26 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 3.9409215E-06 5.7983398E-04 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 13:59:26 3.516u 0.162s 0:04.12 89.0% 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 Mon Oct 10 2011 at 13:59:27 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.721831 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): -11.10400 50.92300 ymin,ymax (A): -13.23600 42.47000 zmin,zma (A): 19.31800 75.58100 x,y,z range (A): 62.02700 55.70600 56.26300 scale (grids/A): 1.721831 object centre (A): 19.90950 14.61700 47.44950 number of atom coordinates read : 3366 total number of charged atoms : 3209 net assigned charge : 4.240020 assigned positive charge : 520.1039 centred at (gu) : 92.71128 89.57438 83.42092 assigned negative charge : -515.8651 centred at (gu) : 92.30541 89.82803 83.35667 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 80812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31439 grid for indexing accessible points = 1.400000 m= 26942 mr = 54176 m= 3608 mr = 18285 m= 147 mr = 1802 m= 0 mr = 25 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 37221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 277 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 24809 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) : 0.5739436 object centre at (A) : 19.90950 14.61700 47.44950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0957537E-02 6.6122580E-03 midg,1,midg; midg,igrid,midg 2.1431390E-02 -9.4139660E-03 1,midg,midg; igrid,midg,midg -1.0328968E-02 1.9423636E-02 gauss-seidel spectral radius is 0.9984154 estimated iterations to convergence 199 setup time was (sec) 0.9800000 now iterating at: 13:59:28 rms-change max change #iterations 4.105034 175.6438 at 10iterations 1.810085 62.55181 at 20iterations 0.8029616 27.67697 at 30iterations 0.3557796 12.20231 at 40iterations 0.1578499 5.568666 at 50iterations 6.9737993E-02 2.448335 at 60iterations 3.0963454E-02 1.149316 at 70iterations 1.3740155E-02 0.4583907 at 80iterations 6.0925600E-03 0.1885781 at 90iterations 2.7094095E-03 9.2704773E-02 at 100iterations 1.2035290E-03 3.9372444E-02 at 110iterations 5.4344838E-04 1.8136978E-02 at 120iterations finished qdiffx linear iterations at : 13:59:35 total time elapsed so far: 8.130000 # loops : 120 mean,max change (kT/e) : 5.4344838E-04 1.8136978E-02 energy calculations done at 8.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.350000 DelPhi exited at 13:59:36 8.356u 0.237s 0:09.51 90.2% 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 Mon Oct 10 2011 at 13:59:36 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.582746 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): -11.10400 50.92300 ymin,ymax (A): -13.23600 42.47000 zmin,zma (A): 19.31800 75.58100 x,y,z range (A): 62.02700 55.70600 56.26300 scale (grids/A): 2.582746 object centre (A): 19.90950 14.61700 47.44950 number of atom coordinates read : 3366 total number of charged atoms : 3209 net assigned charge : 4.240020 assigned positive charge : 520.1039 centred at (gu) : 94.06671 89.36135 80.13125 assigned negative charge : -515.8651 centred at (gu) : 93.45802 89.74187 80.03487 start vw surface at 0.2000000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 187198 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31439 grid for indexing accessible points = 1.400000 m= 90523 mr = 132952 m= 29001 mr = 70680 m= 5784 mr = 21438 m= 621 mr = 3826 m= 37 mr = 327 m= 0 mr = 2 time to grow re-entrant surface = 0.9300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.590000 number of dielectric boundary points 83939 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 25635 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) : 1.721831 object centre at (A) : 19.90950 14.61700 47.44950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3883552 8.1339851E-02 midg,1,midg; midg,igrid,midg 0.3355687 -0.1479105 1,midg,midg; igrid,midg,midg 8.4363706E-02 0.2254311 gauss-seidel spectral radius is 0.9992228 estimated iterations to convergence 283 setup time was (sec) 1.900000 now iterating at: 13:59:39 rms-change max change #iterations 10.41105 312.1671 at 10iterations 6.129854 158.2735 at 20iterations 3.563442 78.51710 at 30iterations 2.063789 47.47732 at 40iterations 1.187492 24.20529 at 50iterations 0.6816419 18.23794 at 60iterations 0.3907053 8.093535 at 70iterations 0.2232401 4.359644 at 80iterations 0.1273807 2.446623 at 90iterations 7.2845876E-02 1.459123 at 100iterations 4.1402765E-02 0.9429893 at 110iterations 2.3594413E-02 0.4833946 at 120iterations 1.3466726E-02 0.2565002 at 130iterations 7.6478743E-03 0.1493702 at 140iterations 4.3900311E-03 8.8585854E-02 at 150iterations 2.5291543E-03 5.0406456E-02 at 160iterations 1.4964410E-03 3.1801224E-02 at 170iterations 9.2012988E-04 1.7719746E-02 at 180iterations finished qdiffx linear iterations at : 13:59:49 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 9.2012988E-04 1.7719746E-02 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 13:59:50 12.407u 0.222s 0:13.49 93.5% 0+0k 0+0io 0pf+0w