Tue Oct 11 05:59:04 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 05:59:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6718503 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): 2.665000 47.75400 ymin,ymax (A): -26.72300 12.33800 zmin,zma (A): -2.809000 50.17900 x,y,z range (A): 45.08900 39.06100 52.98800 scale (grids/A): 0.6718503 object centre (A): 25.20950 -7.192500 23.68500 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 90.07306 90.30044 89.45034 assigned negative charge : -305.3172 centred at (gu) : 90.24194 90.27837 89.47636 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6215 nv = 96 ne = 84 npr = 41995 no. pairs analyzed = 41995 no. exposed pairs = 2499 no. arc points = 17155 no. surface atoms = 856 nbur = 1209 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 374 mr = 3505 m= 2 mr = 47 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 0.1700000 number of dielectric boundary points 3039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1724 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7230 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5255830E-08 1.8582341E-08 midg,1,midg; midg,igrid,midg 2.0280977E-08 3.2660811E-08 1,midg,midg; igrid,midg,midg 6.0051946E-08 -1.0096582E-08 gauss-seidel spectral radius is 0.9884610 estimated iterations to convergence 76 setup time was (sec) 0.3500000 now iterating at: 05:59:05 rms-change max change #iterations 0.1555835 26.99717 at 10iterations 1.7404072E-02 2.516120 at 20iterations 2.0917200E-03 0.3025017 at 30iterations 3.2624742E-04 4.7071457E-02 at 40iterations 7.2729985E-05 1.0725021E-02 at 50iterations finished qdiffx linear iterations at : 05:59:08 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 7.2729985E-05 1.0725021E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 05:59:09 3.319u 0.169s 0:04.25 81.6% 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 05:59:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.015551 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): 2.665000 47.75400 ymin,ymax (A): -26.72300 12.33800 zmin,zma (A): -2.809000 50.17900 x,y,z range (A): 45.08900 39.06100 52.98800 scale (grids/A): 2.015551 object centre (A): 25.20950 -7.192500 23.68500 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 90.21929 90.90129 88.35099 assigned negative charge : -305.3172 centred at (gu) : 90.72604 90.83536 88.42929 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 66986 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17155 grid for indexing accessible points = 1.400000 m= 25376 mr = 47313 m= 4169 mr = 18943 m= 283 mr = 2543 m= 3 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 27907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 15326 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) : 0.6718503 object centre at (A) : 25.20950 -7.192500 23.68500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4056319E-02 5.0428845E-02 midg,1,midg; midg,igrid,midg 4.5609679E-03 2.0229584E-02 1,midg,midg; igrid,midg,midg 3.2200478E-02 6.2440438E-03 gauss-seidel spectral radius is 0.9987164 estimated iterations to convergence 221 setup time was (sec) 0.5300000 now iterating at: 05:59:09 rms-change max change #iterations 4.118564 230.0289 at 10iterations 1.978106 65.90022 at 20iterations 0.9491709 31.25590 at 30iterations 0.4563825 16.51058 at 40iterations 0.2191188 7.732816 at 50iterations 0.1054318 3.373528 at 60iterations 5.0705817E-02 1.702379 at 70iterations 2.4348108E-02 0.7771187 at 80iterations 1.1772778E-02 0.3821602 at 90iterations 5.7141138E-03 0.1807251 at 100iterations 2.7824275E-03 9.0602875E-02 at 110iterations 1.3844887E-03 4.6047211E-02 at 120iterations finished qdiffx linear iterations at : 05:59:16 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 1.3844887E-03 4.6047211E-02 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 05:59:17 7.648u 0.204s 0:08.39 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 05:59:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 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: 3.023326 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): 2.665000 47.75400 ymin,ymax (A): -26.72300 12.33800 zmin,zma (A): -2.809000 50.17900 x,y,z range (A): 45.08900 39.06100 52.98800 scale (grids/A): 3.023326 object centre (A): 25.20950 -7.192500 23.68500 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 90.32882 91.35194 87.52651 assigned negative charge : -305.3172 centred at (gu) : 91.08920 91.25294 87.64397 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 154613 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17155 grid for indexing accessible points = 1.400000 m= 81450 mr = 114130 m= 30232 mr = 67286 m= 7563 mr = 24330 m= 1181 mr = 5618 m= 68 mr = 800 m= 0 mr = 29 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9000000 number of dielectric boundary points 62914 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 15496 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) : 2.015551 object centre at (A) : 25.20950 -7.192500 23.68500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3429158 0.6627636 midg,1,midg; midg,igrid,midg 2.5456438E-02 0.1749549 1,midg,midg; igrid,midg,midg 0.2628226 8.8107355E-02 gauss-seidel spectral radius is 0.9992647 estimated iterations to convergence 291 setup time was (sec) 1.120000 now iterating at: 05:59:19 rms-change max change #iterations 9.495556 473.8597 at 10iterations 5.543455 149.3343 at 20iterations 3.232826 79.07361 at 30iterations 1.875045 43.83170 at 40iterations 1.091861 21.77270 at 50iterations 0.6330078 12.10898 at 60iterations 0.3682182 7.505877 at 70iterations 0.2126002 4.108932 at 80iterations 0.1228636 2.657259 at 90iterations 7.1208403E-02 1.351582 at 100iterations 4.1190717E-02 0.7492275 at 110iterations 2.3963913E-02 0.4726646 at 120iterations 1.3987991E-02 0.2811407 at 130iterations 8.2393577E-03 0.1569655 at 140iterations 4.9291062E-03 9.3083501E-02 at 150iterations 3.0381817E-03 6.1212540E-02 at 160iterations 1.9535865E-03 3.6643982E-02 at 170iterations 1.3263690E-03 2.4940491E-02 at 180iterations finished qdiffx linear iterations at : 05:59:30 total time elapsed so far: 12.31000 # loops : 180 mean,max change (kT/e) : 1.3263690E-03 2.4940491E-02 energy calculations done at 12.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.44000 DelPhi exited at 05:59:31 12.443u 0.208s 0:13.34 94.7% 0+0k 0+0io 0pf+0w