Mon Oct 10 21:10:56 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 21:10:56 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2443 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: 0.6783795 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): -22.46800 26.79100 ymin,ymax (A): 2.541000 46.31000 zmin,zma (A): -2.276000 50.20200 x,y,z range (A): 49.25900 43.76900 52.47800 scale (grids/A): 0.6783795 object centre (A): 2.161500 24.42550 23.96300 number of atom coordinates read : 2443 total number of charged atoms : 2309 net assigned charge : -0.9999914 assigned positive charge : 355.1971 centred at (gu) : 90.90260 91.53346 91.04777 assigned negative charge : -356.1980 centred at (gu) : 90.84695 91.43938 91.06348 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7596 nv = 96 ne = 84 npr = 50418 no. pairs analyzed = 50418 no. exposed pairs = 3313 no. arc points = 22591 no. surface atoms = 1114 nbur = 1329 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 478 mr = 4006 m= 2 mr = 57 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 0.3700000 number of dielectric boundary points 4013 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2053 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8783 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8285572E-10 -1.1341815E-08 midg,1,midg; midg,igrid,midg -2.3286963E-08 3.0400823E-08 1,midg,midg; igrid,midg,midg -1.7196673E-08 1.3521648E-08 gauss-seidel spectral radius is 0.9887245 estimated iterations to convergence 77 setup time was (sec) 0.6700000 now iterating at: 21:10:57 rms-change max change #iterations 0.1791272 24.63273 at 10iterations 1.9786524E-02 2.877798 at 20iterations 2.3222363E-03 0.3286724 at 30iterations 2.7898717E-04 3.8689613E-02 at 40iterations 3.9708015E-05 5.1736832E-03 at 50iterations finished qdiffx linear iterations at : 21:11:00 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 3.9708015E-05 5.1736832E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.290000 DelPhi exited at 21:11:01 4.293u 0.231s 0:04.91 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 Mon Oct 10 2011 at 21:11:01 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2443 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: 2.035139 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): -22.46800 26.79100 ymin,ymax (A): 2.541000 46.31000 zmin,zma (A): -2.276000 50.20200 x,y,z range (A): 49.25900 43.76900 52.47800 scale (grids/A): 2.035139 object centre (A): 2.161500 24.42550 23.96300 number of atom coordinates read : 2443 total number of charged atoms : 2309 net assigned charge : -0.9999914 assigned positive charge : 355.1971 centred at (gu) : 92.70708 94.60020 93.14285 assigned negative charge : -356.1980 centred at (gu) : 92.54095 94.31812 93.19054 start vw surface at 0.2200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 81254 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22591 grid for indexing accessible points = 1.400000 m= 30660 mr = 55418 m= 5902 mr = 22109 m= 437 mr = 3705 m= 10 mr = 140 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 36892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 18296 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) : 0.6783795 object centre at (A) : 2.161500 24.42550 23.96300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4815018E-02 -6.2065539E-03 midg,1,midg; midg,igrid,midg -1.6815791E-02 1.6187488E-03 1,midg,midg; igrid,midg,midg 8.5217599E-03 2.5427790E-02 gauss-seidel spectral radius is 0.9987857 estimated iterations to convergence 227 setup time was (sec) 1.200000 now iterating at: 21:11:03 rms-change max change #iterations 4.581316 177.0138 at 10iterations 2.232442 75.81200 at 20iterations 1.088120 32.16370 at 30iterations 0.5337140 16.28481 at 40iterations 0.2597944 7.859665 at 50iterations 0.1269783 3.548155 at 60iterations 6.2183958E-02 1.834782 at 70iterations 3.0263865E-02 0.8757358 at 80iterations 1.4815271E-02 0.4879971 at 90iterations 7.2464314E-03 0.2245007 at 100iterations 3.5666060E-03 0.1131325 at 110iterations 1.7504011E-03 5.2421570E-02 at 120iterations finished qdiffx linear iterations at : 21:11:11 total time elapsed so far: 9.710000 # loops : 120 mean,max change (kT/e) : 1.7504011E-03 5.2421570E-02 energy calculations done at 9.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.940000 DelPhi exited at 21:11:12 9.944u 0.271s 0:10.71 95.3% 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 Mon Oct 10 2011 at 21:11:12 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2443 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: 3.052708 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): -22.46800 26.79100 ymin,ymax (A): 2.541000 46.31000 zmin,zma (A): -2.276000 50.20200 x,y,z range (A): 49.25900 43.76900 52.47800 scale (grids/A): 3.052708 object centre (A): 2.161500 24.42550 23.96300 number of atom coordinates read : 2443 total number of charged atoms : 2309 net assigned charge : -0.9999914 assigned positive charge : 355.1971 centred at (gu) : 94.06052 96.90028 94.71414 assigned negative charge : -356.1980 centred at (gu) : 93.81150 96.47711 94.78561 start vw surface at 0.1900000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 187914 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22591 grid for indexing accessible points = 1.400000 m= 95425 mr = 134919 m= 38550 mr = 76820 m= 10927 mr = 30560 m= 1912 mr = 8144 m= 95 mr = 1267 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.030000 number of dielectric boundary points 83084 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.220000 number of grid points assigned charge 18472 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) : 2.035139 object centre at (A) : 2.161500 24.42550 23.96300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3848797E-03 -0.1233111 midg,1,midg; midg,igrid,midg -0.1491113 -0.1176021 1,midg,midg; igrid,midg,midg 0.2331280 0.3031361 gauss-seidel spectral radius is 0.9993070 estimated iterations to convergence 300 setup time was (sec) 2.450000 now iterating at: 21:11:14 rms-change max change #iterations 10.66765 410.1639 at 10iterations 6.409902 166.0580 at 20iterations 3.830116 76.73911 at 30iterations 2.278563 50.10740 at 40iterations 1.347596 26.43700 at 50iterations 0.7967462 15.27455 at 60iterations 0.4694587 8.295773 at 70iterations 0.2767088 4.720829 at 80iterations 0.1627968 2.676847 at 90iterations 9.5514685E-02 1.526947 at 100iterations 5.6113832E-02 0.9509296 at 110iterations 3.2812346E-02 0.5407190 at 120iterations 1.9263849E-02 0.3347597 at 130iterations 1.1320194E-02 0.1984427 at 140iterations 6.6533708E-03 0.1136589 at 150iterations 3.9143711E-03 7.0365906E-02 at 160iterations 2.3173548E-03 4.0324211E-02 at 170iterations 1.3805097E-03 2.3529053E-02 at 180iterations finished qdiffx linear iterations at : 21:11:28 total time elapsed so far: 16.23000 # loops : 180 mean,max change (kT/e) : 1.3805097E-03 2.3529053E-02 energy calculations done at 16.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.49000 DelPhi exited at 21:11:29 16.492u 0.256s 0:17.40 96.2% 0+0k 0+0io 0pf+0w