Mon Oct 10 16:26:24 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 Mon Oct 10 2011 at 16:26:24 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 = 2579 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: 0.5737032 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): 60.47500 112.3620 ymin,ymax (A): 224.9630 287.0160 zmin,zma (A): 79.21200 127.3290 x,y,z range (A): 51.88700 62.05299 48.11700 scale (grids/A): 0.5737032 object centre (A): 86.41850 255.9895 103.2705 number of atom coordinates read : 2579 total number of charged atoms : 2436 net assigned charge : 7.000030 assigned positive charge : 388.9645 centred at (gu) : 90.54423 89.81884 91.77798 assigned negative charge : -381.9654 centred at (gu) : 90.41431 89.65935 91.89271 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5485 nv = 96 ne = 84 npr = 50367 no. pairs analyzed = 50367 no. exposed pairs = 3555 no. arc points = 25427 no. surface atoms = 1174 nbur = 1405 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 = 1.484000 m= 278 mr = 2637 m= 0 mr = 22 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3104 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2519 ## 344 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7067 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9677548E-09 -8.4351887E-10 midg,1,midg; midg,igrid,midg -1.2840935E-09 3.4877048E-09 1,midg,midg; igrid,midg,midg -6.5932598E-10 3.6457393E-09 gauss-seidel spectral radius is 0.9842935 estimated iterations to convergence 66 setup time was (sec) 0.6100000 now iterating at: 16:26:25 rms-change max change #iterations 8.5177176E-02 14.76112 at 10iterations 6.4765681E-03 1.022564 at 20iterations 4.8129237E-04 7.7983856E-02 at 30iterations 3.7362377E-05 6.5574646E-03 at 40iterations 2.8074933E-06 4.8160553E-04 at 50iterations finished qdiffx linear iterations at : 16:26:29 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 2.8074933E-06 4.8160553E-04 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 16:26:29 4.182u 0.291s 0:04.88 91.5% 0+0k 0+0io 6pf+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 Mon Oct 10 2011 at 16:26:29 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 = 2579 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: 1.721110 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): 60.47500 112.3620 ymin,ymax (A): 224.9630 287.0160 zmin,zma (A): 79.21200 127.3290 x,y,z range (A): 51.88700 62.05299 48.11700 scale (grids/A): 1.721110 object centre (A): 86.41850 255.9895 103.2705 number of atom coordinates read : 2579 total number of charged atoms : 2436 net assigned charge : 7.000030 assigned positive charge : 388.9645 centred at (gu) : 91.63171 89.45580 95.33344 assigned negative charge : -381.9654 centred at (gu) : 91.24254 88.97787 95.67770 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 59196 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25427 grid for indexing accessible points = 1.400000 m= 19441 mr = 37640 m= 2690 mr = 13443 m= 84 mr = 1502 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 123 time to turn everything in is 0.5500000 number of dielectric boundary points 28814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 248 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 18864 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) : 0.5737032 object centre at (A) : 86.41850 255.9895 103.2705 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8597342E-03 -1.0164371E-02 midg,1,midg; midg,igrid,midg 2.3365668E-03 6.4111506E-03 1,midg,midg; igrid,midg,midg 4.8876624E-03 1.5745139E-02 gauss-seidel spectral radius is 0.9983336 estimated iterations to convergence 194 setup time was (sec) 0.8700000 now iterating at: 16:26:30 rms-change max change #iterations 3.408509 158.9834 at 10iterations 1.468351 66.04631 at 20iterations 0.6343760 23.40166 at 30iterations 0.2735422 10.01541 at 40iterations 0.1179900 4.218407 at 50iterations 5.1017374E-02 1.761066 at 60iterations 2.2145754E-02 0.8002748 at 70iterations 9.5634451E-03 0.3452454 at 80iterations 4.1401023E-03 0.1976230 at 90iterations 1.7854614E-03 6.8435669E-02 at 100iterations 7.7640690E-04 3.0569434E-02 at 110iterations 3.3546242E-04 1.2060881E-02 at 120iterations finished qdiffx linear iterations at : 16:26:39 total time elapsed so far: 9.360000 # loops : 120 mean,max change (kT/e) : 3.3546242E-04 1.2060881E-02 energy calculations done at 9.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.540000 DelPhi exited at 16:26:39 9.543u 0.323s 0:10.19 96.7% 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 Mon Oct 10 2011 at 16:26:39 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 = 2579 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: 2.581664 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): 60.47500 112.3620 ymin,ymax (A): 224.9630 287.0160 zmin,zma (A): 79.21200 127.3290 x,y,z range (A): 51.88700 62.05299 48.11700 scale (grids/A): 2.581664 object centre (A): 86.41850 255.9895 103.2705 number of atom coordinates read : 2579 total number of charged atoms : 2436 net assigned charge : 7.000030 assigned positive charge : 388.9645 centred at (gu) : 92.44758 89.18349 97.99986 assigned negative charge : -381.9654 centred at (gu) : 91.86384 88.46673 98.51649 start vw surface at 0.1600000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 136951 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25427 grid for indexing accessible points = 1.400000 m= 63116 mr = 92365 m= 21800 mr = 49049 m= 4403 mr = 16938 m= 410 mr = 3084 m= 9 mr = 201 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 404 time to turn everything in is 1.360000 number of dielectric boundary points 65052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 19473 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) : 1.721110 object centre at (A) : 86.41850 255.9895 103.2705 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9603277E-02 -0.1435903 midg,1,midg; midg,igrid,midg 3.1391822E-02 -0.3932686 1,midg,midg; igrid,midg,midg 5.2922826E-02 0.1492216 gauss-seidel spectral radius is 0.9991762 estimated iterations to convergence 275 setup time was (sec) 1.690000 now iterating at: 16:26:41 rms-change max change #iterations 8.621005 284.2955 at 10iterations 4.892134 136.4744 at 20iterations 2.743648 61.65099 at 30iterations 1.539014 37.15820 at 40iterations 0.8592030 20.62739 at 50iterations 0.4801274 10.97328 at 60iterations 0.2677442 6.320762 at 70iterations 0.1488286 3.249074 at 80iterations 8.2866482E-02 1.682034 at 90iterations 4.6171319E-02 1.041153 at 100iterations 2.5674170E-02 0.5143566 at 110iterations 1.4261155E-02 0.3142627 at 120iterations 7.9470444E-03 0.1650975 at 130iterations 4.4154185E-03 9.8111153E-02 at 140iterations 2.4534892E-03 5.2125454E-02 at 150iterations 1.3663542E-03 3.1267166E-02 at 160iterations 7.5884903E-04 1.6206741E-02 at 170iterations 4.2345078E-04 9.1209412E-03 at 180iterations finished qdiffx linear iterations at : 16:26:55 total time elapsed so far: 15.45000 # loops : 180 mean,max change (kT/e) : 4.2345078E-04 9.1209412E-03 energy calculations done at 15.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.63000 DelPhi exited at 16:26:56 15.634u 0.339s 0:16.30 97.9% 0+0k 0+0io 0pf+0w