Tue Oct 11 03:41:15 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 03:41:15 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 = 2729 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6771794 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): -46.62000 0.8000000 ymin,ymax (A): -47.43700 1.676000 zmin,zma (A): -6.993000 45.57800 x,y,z range (A): 47.42000 49.11300 52.57100 scale (grids/A): 0.6771794 object centre (A): -22.91000 -22.88050 19.29250 number of atom coordinates read : 2729 total number of charged atoms : 2578 net assigned charge : 4.140013 assigned positive charge : 410.9867 centred at (gu) : 89.97579 90.53648 91.01669 assigned negative charge : -406.8474 centred at (gu) : 89.70103 90.35114 91.00808 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8492 nv = 96 ne = 84 npr = 55882 no. pairs analyzed = 55882 no. exposed pairs = 3294 no. arc points = 23010 no. surface atoms = 1106 nbur = 1623 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 520 mr = 4899 m= 2 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 36 time to turn everything in is 0.3700000 number of dielectric boundary points 4040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2100 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9615 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1213492E-08 2.3386683E-08 midg,1,midg; midg,igrid,midg -3.9070997E-08 8.2902723E-08 1,midg,midg; igrid,midg,midg -7.4002003E-08 1.0087954E-07 gauss-seidel spectral radius is 0.9887049 estimated iterations to convergence 77 setup time was (sec) 0.6200000 now iterating at: 03:41:16 rms-change max change #iterations 0.1889631 27.88634 at 10iterations 2.1190304E-02 2.731249 at 20iterations 2.5014021E-03 0.3163757 at 30iterations 3.0985061E-04 4.2503357E-02 at 40iterations 5.3325799E-05 7.1458817E-03 at 50iterations finished qdiffx linear iterations at : 03:41:19 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 5.3325799E-05 7.1458817E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 03:41:19 3.719u 0.207s 0:04.44 88.0% 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 Tue Oct 11 2011 at 03:41:19 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 = 2729 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.031538 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): -46.62000 0.8000000 ymin,ymax (A): -47.43700 1.676000 zmin,zma (A): -6.993000 45.57800 x,y,z range (A): 47.42000 49.11300 52.57100 scale (grids/A): 2.031538 object centre (A): -22.91000 -22.88050 19.29250 number of atom coordinates read : 2729 total number of charged atoms : 2578 net assigned charge : 4.140013 assigned positive charge : 410.9867 centred at (gu) : 89.92679 91.60921 93.04903 assigned negative charge : -406.8474 centred at (gu) : 89.10308 91.05311 93.02410 start vw surface at 0.1800000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 90865 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23010 grid for indexing accessible points = 1.400000 m= 36341 mr = 64834 m= 6689 mr = 27913 m= 494 mr = 4391 m= 8 mr = 254 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 2631 time to turn everything in is 0.7400000 number of dielectric boundary points 37005 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 20427 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) : 0.6771794 object centre at (A) : -22.91000 -22.88050 19.29250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5516403E-02 1.1606609E-02 midg,1,midg; midg,igrid,midg -1.2994367E-02 4.1033790E-02 1,midg,midg; igrid,midg,midg -1.8043779E-02 7.9193607E-02 gauss-seidel spectral radius is 0.9988041 estimated iterations to convergence 229 setup time was (sec) 1.070000 now iterating at: 03:41:21 rms-change max change #iterations 4.963199 222.1373 at 10iterations 2.448694 106.6404 at 20iterations 1.197986 33.04023 at 30iterations 0.5922872 17.57406 at 40iterations 0.2913848 8.783760 at 50iterations 0.1440452 4.316525 at 60iterations 7.0841953E-02 1.906097 at 70iterations 3.4875851E-02 0.9065628 at 80iterations 1.7240897E-02 0.5037680 at 90iterations 8.4807230E-03 0.2451973 at 100iterations 4.1804649E-03 0.1182556 at 110iterations 2.0663540E-03 6.1727524E-02 at 120iterations finished qdiffx linear iterations at : 03:41:28 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 2.0663540E-03 6.1727524E-02 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 03:41:28 8.293u 0.239s 0:09.03 94.3% 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 03:41:28 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 = 2729 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 3.047307 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): -46.62000 0.8000000 ymin,ymax (A): -47.43700 1.676000 zmin,zma (A): -6.993000 45.57800 x,y,z range (A): 47.42000 49.11300 52.57100 scale (grids/A): 3.047307 object centre (A): -22.91000 -22.88050 19.29250 number of atom coordinates read : 2729 total number of charged atoms : 2578 net assigned charge : 4.140013 assigned positive charge : 410.9867 centred at (gu) : 89.88995 92.41371 94.57335 assigned negative charge : -406.8474 centred at (gu) : 88.65456 91.57962 94.53610 start vw surface at 0.1800000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 209492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23010 grid for indexing accessible points = 1.400000 m= 114156 mr = 156014 m= 45542 mr = 95634 m= 12232 mr = 37578 m= 2130 mr = 9541 m= 183 mr = 1580 m= 5 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 8784 time to turn everything in is 1.840000 number of dielectric boundary points 83288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 20616 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) : 2.031538 object centre at (A) : -22.91000 -22.88050 19.29250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0889601E-02 0.3922113 midg,1,midg; midg,igrid,midg -0.1376481 0.4579701 1,midg,midg; igrid,midg,midg -7.0987940E-02 0.5785418 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 2.190000 now iterating at: 03:41:31 rms-change max change #iterations 11.22509 378.0776 at 10iterations 6.623372 149.6698 at 20iterations 3.920274 90.48192 at 30iterations 2.311222 55.11740 at 40iterations 1.358781 23.77174 at 50iterations 0.8002700 13.84595 at 60iterations 0.4692664 8.672441 at 70iterations 0.2751669 4.748655 at 80iterations 0.1615274 2.657347 at 90iterations 9.4571054E-02 1.581935 at 100iterations 5.5411600E-02 0.8923626 at 110iterations 3.2395292E-02 0.5240593 at 120iterations 1.8988639E-02 0.3317506 at 130iterations 1.1156142E-02 0.1851044 at 140iterations 6.5626646E-03 0.1075487 at 150iterations 3.8781182E-03 6.8042755E-02 at 160iterations 2.3101142E-03 3.9367676E-02 at 170iterations 1.3975385E-03 2.4398804E-02 at 180iterations finished qdiffx linear iterations at : 03:41:42 total time elapsed so far: 13.53000 # loops : 180 mean,max change (kT/e) : 1.3975385E-03 2.4398804E-02 energy calculations done at 13.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.71000 DelPhi exited at 03:41:43 13.716u 0.267s 0:14.28 97.8% 0+0k 0+0io 0pf+0w