Sat Oct 8 11:33:50 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 Sat Oct 8 2011 at 11:33:50 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2312 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: 0.6600904 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): -60.45900 -10.71600 ymin,ymax (A): 53.97600 102.4800 zmin,zma (A): 39.07800 93.01000 x,y,z range (A): 49.74300 48.50399 53.93200 scale (grids/A): 0.6600904 object centre (A): -35.58750 78.22800 66.04400 number of atom coordinates read : 2312 total number of charged atoms : 2155 net assigned charge : -0.9999928 assigned positive charge : 331.1084 centred at (gu) : 91.78162 90.48299 91.65188 assigned negative charge : -332.1086 centred at (gu) : 91.70115 90.46793 91.65543 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7049 nv = 96 ne = 84 npr = 47128 no. pairs analyzed = 47128 no. exposed pairs = 3076 no. arc points = 21499 no. surface atoms = 1038 nbur = 1274 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 408 mr = 3775 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1995 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7984 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5908361E-09 -4.7732986E-09 midg,1,midg; midg,igrid,midg -4.8381343E-09 -2.7716732E-10 1,midg,midg; igrid,midg,midg -1.1375525E-08 1.5696031E-08 gauss-seidel spectral radius is 0.9880878 estimated iterations to convergence 75 setup time was (sec) 0.4300000 now iterating at: 11:33:51 rms-change max change #iterations 0.1520648 20.41150 at 10iterations 1.6457209E-02 2.501587 at 20iterations 1.7270300E-03 0.2493496 at 30iterations 1.8166663E-04 2.7145386E-02 at 40iterations 1.9675546E-05 2.9811859E-03 at 50iterations finished qdiffx linear iterations at : 11:33:54 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 1.9675546E-05 2.9811859E-03 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 11:33:55 3.932u 0.248s 0:04.57 91.2% 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 Sat Oct 8 2011 at 11:33:55 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2312 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: 1.980271 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): -60.45900 -10.71600 ymin,ymax (A): 53.97600 102.4800 zmin,zma (A): 39.07800 93.01000 x,y,z range (A): 49.74300 48.50399 53.93200 scale (grids/A): 1.980271 object centre (A): -35.58750 78.22800 66.04400 number of atom coordinates read : 2312 total number of charged atoms : 2155 net assigned charge : -0.9999928 assigned positive charge : 331.1084 centred at (gu) : 95.34459 91.44888 94.95538 assigned negative charge : -332.1086 centred at (gu) : 95.10326 91.40354 94.96607 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 75125 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21499 grid for indexing accessible points = 1.400000 m= 26753 mr = 50892 m= 4288 mr = 19354 m= 259 mr = 2601 m= 8 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 33499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 17032 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) : 0.6600904 object centre at (A) : -35.58750 78.22800 66.04400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3910286E-02 4.0898286E-03 midg,1,midg; midg,igrid,midg -1.4710602E-02 -1.5355110E-02 1,midg,midg; igrid,midg,midg -9.2621231E-03 2.5771100E-02 gauss-seidel spectral radius is 0.9987088 estimated iterations to convergence 220 setup time was (sec) 0.6500000 now iterating at: 11:33:56 rms-change max change #iterations 4.140932 175.6127 at 10iterations 1.971455 75.99325 at 20iterations 0.9425016 30.15610 at 30iterations 0.4478180 14.71140 at 40iterations 0.2148555 7.960381 at 50iterations 0.1025894 3.082703 at 60iterations 4.8837528E-02 1.507184 at 70iterations 2.3247091E-02 0.7650013 at 80iterations 1.1144153E-02 0.3510761 at 90iterations 5.3037852E-03 0.1626754 at 100iterations 2.5374857E-03 9.1185570E-02 at 110iterations 1.2135830E-03 4.2400360E-02 at 120iterations finished qdiffx linear iterations at : 11:34:04 total time elapsed so far: 8.880000 # loops : 120 mean,max change (kT/e) : 1.2135830E-03 4.2400360E-02 energy calculations done at 8.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.010000 DelPhi exited at 11:34:05 9.017u 0.286s 0:10.24 90.7% 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 Sat Oct 8 2011 at 11:34:05 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2312 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: 2.970407 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): -60.45900 -10.71600 ymin,ymax (A): 53.97600 102.4800 zmin,zma (A): 39.07800 93.01000 x,y,z range (A): 49.74300 48.50399 53.93200 scale (grids/A): 2.970407 object centre (A): -35.58750 78.22800 66.04400 number of atom coordinates read : 2312 total number of charged atoms : 2155 net assigned charge : -0.9999928 assigned positive charge : 331.1084 centred at (gu) : 98.01673 92.17323 97.43292 assigned negative charge : -332.1086 centred at (gu) : 97.65489 92.10526 97.44907 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 173785 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21499 grid for indexing accessible points = 1.400000 m= 86057 mr = 123853 m= 31234 mr = 69500 m= 7587 mr = 24605 m= 1134 mr = 5607 m= 69 mr = 708 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.050000 number of dielectric boundary points 75568 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 17240 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) : 1.980271 object centre at (A) : -35.58750 78.22800 66.04400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3941993 -2.7189732E-02 midg,1,midg; midg,igrid,midg -0.1287578 -0.1684543 1,midg,midg; igrid,midg,midg -0.1259868 0.2689165 gauss-seidel spectral radius is 0.9992833 estimated iterations to convergence 295 setup time was (sec) 1.360000 now iterating at: 11:34:07 rms-change max change #iterations 9.763580 417.3375 at 10iterations 5.778298 137.6464 at 20iterations 3.405912 81.70513 at 30iterations 2.000944 44.83629 at 40iterations 1.168629 27.85008 at 50iterations 0.6842891 14.13708 at 60iterations 0.3993650 8.008716 at 70iterations 0.2329511 4.464715 at 80iterations 0.1354070 2.618697 at 90iterations 7.8659944E-02 1.582323 at 100iterations 4.5678996E-02 0.8693924 at 110iterations 2.6620133E-02 0.5067596 at 120iterations 1.5441163E-02 0.2910805 at 130iterations 8.9726346E-03 0.1768570 at 140iterations 5.1998938E-03 9.8770142E-02 at 150iterations 3.0232049E-03 5.9983850E-02 at 160iterations 1.7507185E-03 3.1677246E-02 at 170iterations 1.0156089E-03 1.9592285E-02 at 180iterations finished qdiffx linear iterations at : 11:34:23 total time elapsed so far: 16.65000 # loops : 180 mean,max change (kT/e) : 1.0156089E-03 1.9592285E-02 energy calculations done at 16.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.79000 DelPhi exited at 11:34:23 16.787u 0.413s 0:18.01 95.4% 0+0k 0+0io 0pf+0w