Tue Oct 11 03:14:17 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 03:14:17 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4130 !!! WARNING: GLM 16 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5638979 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): -27.42600 31.00500 ymin,ymax (A): -25.36900 34.93100 zmin,zma (A): -28.58700 34.54500 x,y,z range (A): 58.43100 60.30000 63.13200 scale (grids/A): 0.5638979 object centre (A): 1.789500 4.781000 2.978999 number of atom coordinates read : 4130 total number of charged atoms : 3985 net assigned charge : -3.593949 assigned positive charge : 620.7560 centred at (gu) : 92.27962 90.63992 90.18931 assigned negative charge : -624.3531 centred at (gu) : 92.25245 90.72546 90.18898 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8782 nv = 96 ne = 84 npr = 81270 no. pairs analyzed = 81270 no. exposed pairs = 5462 no. arc points = 39216 no. surface atoms = 1824 nbur = 2306 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 351 mr = 4426 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2800000 number of dielectric boundary points 4689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4015 ## 539 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 11341 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2631482E-10 -4.5338969E-10 midg,1,midg; midg,igrid,midg 9.0603425E-10 -2.3051192E-09 1,midg,midg; igrid,midg,midg -5.3941440E-10 9.2464640E-11 gauss-seidel spectral radius is 0.9838798 estimated iterations to convergence 65 setup time was (sec) 0.4700000 now iterating at: 03:14:18 rms-change max change #iterations 0.1040622 15.88902 at 10iterations 7.6017263E-03 0.8987055 at 20iterations 6.1095943E-04 8.4686279E-02 at 30iterations 8.2047154E-05 1.3730645E-02 at 40iterations 2.0674906E-05 3.7837625E-03 at 50iterations finished qdiffx linear iterations at : 03:14:21 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 2.0674906E-05 3.7837625E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 03:14:21 3.452u 0.164s 0:03.92 92.0% 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 03:14:21 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4130 !!! WARNING: GLM 16 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.691694 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): -27.42600 31.00500 ymin,ymax (A): -25.36900 34.93100 zmin,zma (A): -28.58700 34.54500 x,y,z range (A): 58.43100 60.30000 63.13200 scale (grids/A): 1.691694 object centre (A): 1.789500 4.781000 2.978999 number of atom coordinates read : 4130 total number of charged atoms : 3985 net assigned charge : -3.593949 assigned positive charge : 620.7560 centred at (gu) : 96.83753 91.91847 90.56629 assigned negative charge : -624.3531 centred at (gu) : 96.75671 92.17595 90.56657 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 96310 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39216 grid for indexing accessible points = 1.400000 m= 30184 mr = 64102 m= 3369 mr = 20621 m= 100 mr = 1668 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 588 time to turn everything in is 0.4500000 number of dielectric boundary points 43563 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 435 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 30751 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) : 0.5638979 object centre at (A) : 1.789500 4.781000 2.978999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2495976E-02 -4.4309475E-02 midg,1,midg; midg,igrid,midg 3.5179020E-03 -2.0356558E-02 1,midg,midg; igrid,midg,midg 5.5805654E-03 2.2076288E-02 gauss-seidel spectral radius is 0.9984401 estimated iterations to convergence 201 setup time was (sec) 0.6800000 now iterating at: 03:14:22 rms-change max change #iterations 4.355419 170.7553 at 10iterations 1.920218 57.06148 at 20iterations 0.8532069 25.47627 at 30iterations 0.3784291 10.94909 at 40iterations 0.1678811 4.758862 at 50iterations 7.4833155E-02 2.544456 at 60iterations 3.3212598E-02 1.055007 at 70iterations 1.4761132E-02 0.4595642 at 80iterations 6.5794825E-03 0.1930807 at 90iterations 2.9321883E-03 9.0091705E-02 at 100iterations 1.2998332E-03 3.8005590E-02 at 110iterations 5.8061036E-04 1.8012047E-02 at 120iterations finished qdiffx linear iterations at : 03:14:29 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 5.8061036E-04 1.8012047E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 03:14:30 8.020u 0.202s 0:08.66 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 03:14:30 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4130 !!! WARNING: GLM 16 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.537540 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): -27.42600 31.00500 ymin,ymax (A): -25.36900 34.93100 zmin,zma (A): -28.58700 34.54500 x,y,z range (A): 58.43100 60.30000 63.13200 scale (grids/A): 2.537540 object centre (A): 1.789500 4.781000 2.978999 number of atom coordinates read : 4130 total number of charged atoms : 3985 net assigned charge : -3.593949 assigned positive charge : 620.7560 centred at (gu) : 100.2559 92.87758 90.84925 assigned negative charge : -624.3531 centred at (gu) : 100.1351 93.26363 90.84971 start vw surface at 0.1000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 223102 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39216 grid for indexing accessible points = 1.400000 m= 103583 mr = 156876 m= 30799 mr = 81396 m= 5413 mr = 22999 m= 422 mr = 3572 m= 6 mr = 192 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 2187 time to turn everything in is 1.120000 number of dielectric boundary points 98290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 31851 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) : 1.691694 object centre at (A) : 1.789500 4.781000 2.978999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3810568 -0.9211439 midg,1,midg; midg,igrid,midg 1.9791495E-02 -0.2547131 1,midg,midg; igrid,midg,midg 5.8923542E-02 0.2811716 gauss-seidel spectral radius is 0.9992546 estimated iterations to convergence 289 setup time was (sec) 1.360000 now iterating at: 03:14:32 rms-change max change #iterations 11.17132 321.0831 at 10iterations 6.626073 161.1017 at 20iterations 3.886421 92.30094 at 30iterations 2.274283 42.02453 at 40iterations 1.325612 29.18299 at 50iterations 0.7688236 18.41385 at 60iterations 0.4446908 7.706078 at 70iterations 0.2570010 4.482368 at 80iterations 0.1484585 2.532593 at 90iterations 8.5480675E-02 1.577566 at 100iterations 4.9233373E-02 0.8689065 at 110iterations 2.8303917E-02 0.4903336 at 120iterations 1.6262688E-02 0.2812185 at 130iterations 9.3743401E-03 0.1679296 at 140iterations 5.3840769E-03 9.1381073E-02 at 150iterations 3.0980948E-03 4.9930573E-02 at 160iterations 1.7818856E-03 3.1732559E-02 at 170iterations 1.0254397E-03 1.7736435E-02 at 180iterations finished qdiffx linear iterations at : 03:14:44 total time elapsed so far: 13.26000 # loops : 180 mean,max change (kT/e) : 1.0254397E-03 1.7736435E-02 energy calculations done at 13.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 03:14:44 13.391u 0.231s 0:13.93 97.7% 0+0k 0+0io 0pf+0w