Tue Oct 11 06:01:26 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+sph2.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 = amb2.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 06:01:26 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2081 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7046016 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): 16.27100 64.09700 ymin,ymax (A): -3.508000 33.47700 zmin,zma (A): 21.51900 72.04400 x,y,z range (A): 47.82600 36.98500 50.52500 scale (grids/A): 0.7046016 object centre (A): 40.18400 14.98450 46.78150 number of atom coordinates read : 2081 total number of charged atoms : 1949 net assigned charge : 6.420009 assigned positive charge : 319.6860 centred at (gu) : 90.86395 89.71107 88.74995 assigned negative charge : -313.2661 centred at (gu) : 90.99324 89.74791 88.69739 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7091 nv = 96 ne = 84 npr = 41484 no. pairs analyzed = 41484 no. exposed pairs = 2517 no. arc points = 17218 no. surface atoms = 857 nbur = 1224 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 475 mr = 4103 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2600000 number of dielectric boundary points 3365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1560 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7791 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3650036E-08 5.9657850E-08 midg,1,midg; midg,igrid,midg 7.2416526E-08 3.2509071E-08 1,midg,midg; igrid,midg,midg 9.3680733E-08 -1.1841683E-08 gauss-seidel spectral radius is 0.9895024 estimated iterations to convergence 79 setup time was (sec) 0.5700000 now iterating at: 06:01:27 rms-change max change #iterations 0.2002583 27.50390 at 10iterations 2.4812136E-02 3.745879 at 20iterations 3.2238793E-03 0.4311600 at 30iterations 5.3251063E-04 6.7272186E-02 at 40iterations 1.2872569E-04 1.7421722E-02 at 50iterations finished qdiffx linear iterations at : 06:01:31 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 1.2872569E-04 1.7421722E-02 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 06:01:32 4.486u 0.384s 0:05.38 90.3% 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 06:01:32 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2081 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.113805 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): 16.27100 64.09700 ymin,ymax (A): -3.508000 33.47700 zmin,zma (A): 21.51900 72.04400 x,y,z range (A): 47.82600 36.98500 50.52500 scale (grids/A): 2.113805 object centre (A): 40.18400 14.98450 46.78150 number of atom coordinates read : 2081 total number of charged atoms : 1949 net assigned charge : 6.420009 assigned positive charge : 319.6860 centred at (gu) : 92.59195 89.13319 86.24983 assigned negative charge : -313.2661 centred at (gu) : 92.97968 89.24383 86.09216 start vw surface at 0.1000000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 75593 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17218 grid for indexing accessible points = 1.400000 m= 31097 mr = 54127 m= 6232 mr = 23935 m= 552 mr = 4218 m= 11 mr = 294 m= 0 mr = 2 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 30909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 15480 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) : 0.7046016 object centre at (A) : 40.18400 14.98450 46.78150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8227767E-02 4.3499593E-02 midg,1,midg; midg,igrid,midg 2.7777405E-02 1.2456944E-02 1,midg,midg; igrid,midg,midg 3.1613391E-02 2.5980106E-02 gauss-seidel spectral radius is 0.9988221 estimated iterations to convergence 231 setup time was (sec) 0.9400000 now iterating at: 06:01:33 rms-change max change #iterations 4.652551 176.9789 at 10iterations 2.306655 72.80061 at 20iterations 1.139175 39.58730 at 30iterations 0.5666830 17.11200 at 40iterations 0.2812750 8.568991 at 50iterations 0.1390037 4.148382 at 60iterations 6.9242068E-02 1.912860 at 70iterations 3.4273822E-02 1.030087 at 80iterations 1.7140828E-02 0.4816475 at 90iterations 8.5836174E-03 0.3153534 at 100iterations 4.3288171E-03 0.1345291 at 110iterations 2.2312554E-03 6.7288160E-02 at 120iterations finished qdiffx linear iterations at : 06:01:43 total time elapsed so far: 10.73000 # loops : 120 mean,max change (kT/e) : 2.2312554E-03 6.7288160E-02 energy calculations done at 10.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.89000 DelPhi exited at 06:01:44 10.899u 0.447s 0:11.93 94.9% 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 06:01:44 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2081 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.170707 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): 16.27100 64.09700 ymin,ymax (A): -3.508000 33.47700 zmin,zma (A): 21.51900 72.04400 x,y,z range (A): 47.82600 36.98500 50.52500 scale (grids/A): 3.170707 object centre (A): 40.18400 14.98450 46.78150 number of atom coordinates read : 2081 total number of charged atoms : 1949 net assigned charge : 6.420009 assigned positive charge : 319.6860 centred at (gu) : 93.88786 88.69986 84.37470 assigned negative charge : -313.2661 centred at (gu) : 94.46953 88.86587 84.13838 start vw surface at 0.1000000 fill in re-entrant regions at 0.7600000 boundary points on vw surface= 174153 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17218 grid for indexing accessible points = 1.400000 m= 96600 mr = 130250 m= 40191 mr = 81085 m= 11846 mr = 33297 m= 2313 mr = 9323 m= 290 mr = 1675 m= 6 mr = 218 m= 0 mr = 2 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.930000 number of dielectric boundary points 69549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 15592 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) : 2.113805 object centre at (A) : 40.18400 14.98450 46.78150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2846126 0.2795954 midg,1,midg; midg,igrid,midg 0.2126313 8.8353343E-02 1,midg,midg; igrid,midg,midg 0.3007396 0.4873334 gauss-seidel spectral radius is 0.9992923 estimated iterations to convergence 297 setup time was (sec) 2.250000 now iterating at: 06:01:46 rms-change max change #iterations 10.35715 347.9258 at 10iterations 6.122160 117.5712 at 20iterations 3.606757 84.99373 at 30iterations 2.127383 55.00256 at 40iterations 1.248135 23.87512 at 50iterations 0.7311770 17.59410 at 60iterations 0.4297830 8.178694 at 70iterations 0.2510999 4.477501 at 80iterations 0.1468178 2.547203 at 90iterations 8.5962787E-02 1.596002 at 100iterations 5.0246343E-02 0.8202553 at 110iterations 2.9528264E-02 0.5164719 at 120iterations 1.7358271E-02 0.3088074 at 130iterations 1.0292087E-02 0.1888299 at 140iterations 6.2074708E-03 0.1062851 at 150iterations 3.8203932E-03 6.1647415E-02 at 160iterations 2.4478897E-03 4.1591644E-02 at 170iterations 1.6531965E-03 2.7538300E-02 at 180iterations finished qdiffx linear iterations at : 06:02:03 total time elapsed so far: 18.85000 # loops : 180 mean,max change (kT/e) : 1.6531965E-03 2.7538300E-02 energy calculations done at 18.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.02000 DelPhi exited at 06:02:04 19.021u 0.475s 0:20.10 96.9% 0+0k 0+0io 0pf+0w