Tue Oct 11 06:39:04 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 06:39:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2056 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: 0.7099128 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): -19.97100 24.60400 ymin,ymax (A): -28.57900 12.07600 zmin,zma (A): -13.40600 36.74100 x,y,z range (A): 44.57500 40.65500 50.14700 scale (grids/A): 0.7099128 object centre (A): 2.316501 -8.251501 11.66750 number of atom coordinates read : 2056 total number of charged atoms : 1928 net assigned charge : 7.500009 assigned positive charge : 311.7690 centred at (gu) : 89.76983 90.26028 89.32262 assigned negative charge : -304.2692 centred at (gu) : 89.59336 90.23462 89.29195 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6980 nv = 96 ne = 84 npr = 41469 no. pairs analyzed = 41469 no. exposed pairs = 2473 no. arc points = 16949 no. surface atoms = 840 nbur = 1216 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 438 mr = 3997 m= 0 mr = 61 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1636 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7834 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8686815E-08 7.3070858E-08 midg,1,midg; midg,igrid,midg 5.1811945E-08 8.4573969E-08 1,midg,midg; igrid,midg,midg -2.5350115E-08 1.4899894E-07 gauss-seidel spectral radius is 0.9896527 estimated iterations to convergence 80 setup time was (sec) 0.4900000 now iterating at: 06:39:05 rms-change max change #iterations 0.1964504 35.50903 at 10iterations 2.4847591E-02 3.384209 at 20iterations 3.2239468E-03 0.4187813 at 30iterations 4.7639111E-04 6.0497284E-02 at 40iterations 1.0086748E-04 1.3654709E-02 at 50iterations finished qdiffx linear iterations at : 06:39:08 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.0086748E-04 1.3654709E-02 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 06:39:08 3.094u 0.147s 0:03.75 86.1% 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 06:39:08 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 = 2056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.129739 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): -19.97100 24.60400 ymin,ymax (A): -28.57900 12.07600 zmin,zma (A): -13.40600 36.74100 x,y,z range (A): 44.57500 40.65500 50.14700 scale (grids/A): 2.129739 object centre (A): 2.316501 -8.251501 11.66750 number of atom coordinates read : 2056 total number of charged atoms : 1928 net assigned charge : 7.500009 assigned positive charge : 311.7690 centred at (gu) : 89.30966 90.78081 87.96794 assigned negative charge : -304.2692 centred at (gu) : 88.78007 90.70412 87.87579 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 74568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16949 grid for indexing accessible points = 1.400000 m= 29600 mr = 53137 m= 5694 mr = 22330 m= 499 mr = 3720 m= 12 mr = 252 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 30934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 15338 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) : 0.7099128 object centre at (A) : 2.316501 -8.251501 11.66750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9854289E-02 4.4717640E-02 midg,1,midg; midg,igrid,midg 4.0591555E-03 3.1809334E-02 1,midg,midg; igrid,midg,midg 1.7601237E-02 4.1036833E-02 gauss-seidel spectral radius is 0.9988358 estimated iterations to convergence 232 setup time was (sec) 0.7800000 now iterating at: 06:39:09 rms-change max change #iterations 4.575658 183.0445 at 10iterations 2.265183 79.04060 at 20iterations 1.126699 34.74391 at 30iterations 0.5588152 16.85562 at 40iterations 0.2790156 8.407269 at 50iterations 0.1389481 4.227464 at 60iterations 6.8892471E-02 2.139198 at 70iterations 3.4307718E-02 1.122593 at 80iterations 1.7091906E-02 0.5213051 at 90iterations 8.5568577E-03 0.2631943 at 100iterations 4.2903246E-03 0.1334209 at 110iterations 2.1729283E-03 6.9376677E-02 at 120iterations finished qdiffx linear iterations at : 06:39:15 total time elapsed so far: 6.920000 # loops : 120 mean,max change (kT/e) : 2.1729283E-03 6.9376677E-02 energy calculations done at 6.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 06:39:16 7.087u 0.163s 0:07.61 95.1% 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 06:39:16 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 = 2056 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.194608 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): -19.97100 24.60400 ymin,ymax (A): -28.57900 12.07600 zmin,zma (A): -13.40600 36.74100 x,y,z range (A): 44.57500 40.65500 50.14700 scale (grids/A): 3.194608 object centre (A): 2.316501 -8.251501 11.66750 number of atom coordinates read : 2056 total number of charged atoms : 1928 net assigned charge : 7.500009 assigned positive charge : 311.7690 centred at (gu) : 88.96448 91.17117 86.95184 assigned negative charge : -304.2692 centred at (gu) : 88.17003 91.05621 86.81380 start vw surface at 0.1300000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 172017 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16949 grid for indexing accessible points = 1.400000 m= 92982 mr = 128017 m= 37491 mr = 77252 m= 10812 mr = 30708 m= 2081 mr = 8355 m= 231 mr = 1474 m= 5 mr = 148 m= 0 mr = 2 time to grow re-entrant surface = 0.8199999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.690000 number of dielectric boundary points 69663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 15424 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) : 2.129739 object centre at (A) : 2.316501 -8.251501 11.66750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7257444 0.3721028 midg,1,midg; midg,igrid,midg 1.7076714E-02 0.2426450 1,midg,midg; igrid,midg,midg 0.2873797 0.3059218 gauss-seidel spectral radius is 0.9992936 estimated iterations to convergence 297 setup time was (sec) 1.970000 now iterating at: 06:39:18 rms-change max change #iterations 10.14436 407.0083 at 10iterations 5.986990 142.5700 at 20iterations 3.535012 72.86647 at 30iterations 2.084635 41.02267 at 40iterations 1.223731 24.07901 at 50iterations 0.7182537 13.74026 at 60iterations 0.4211782 7.644989 at 70iterations 0.2470267 4.691955 at 80iterations 0.1448665 2.677666 at 90iterations 8.4731616E-02 1.587379 at 100iterations 4.9687684E-02 0.8080826 at 110iterations 2.9181356E-02 0.5001545 at 120iterations 1.7218050E-02 0.3177528 at 130iterations 1.0263626E-02 0.1915932 at 140iterations 6.2191444E-03 0.1234264 at 150iterations 3.8676043E-03 7.0880890E-02 at 160iterations 2.5158417E-03 4.8358917E-02 at 170iterations 1.7259633E-03 3.3569336E-02 at 180iterations finished qdiffx linear iterations at : 06:39:27 total time elapsed so far: 11.38000 # loops : 180 mean,max change (kT/e) : 1.7259633E-03 3.3569336E-02 energy calculations done at 11.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 06:39:28 11.550u 0.176s 0:12.21 95.9% 0+0k 0+0io 0pf+0w