Tue Oct 11 07:59:56 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 Tue Oct 11 2011 at 07:59:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2288 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: 0.6591372 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): -57.99000 -3.980000 ymin,ymax (A): 64.01200 108.3240 zmin,zma (A): -24.93200 19.25700 x,y,z range (A): 54.01000 44.31200 44.18900 scale (grids/A): 0.6591372 object centre (A): -30.98500 86.16800 -2.837500 number of atom coordinates read : 2288 total number of charged atoms : 2152 net assigned charge : 4.000010 assigned positive charge : 339.7426 centred at (gu) : 91.03416 91.07230 90.49812 assigned negative charge : -335.7429 centred at (gu) : 91.19667 91.23627 90.46804 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6553 nv = 96 ne = 84 npr = 47207 no. pairs analyzed = 47207 no. exposed pairs = 2681 no. arc points = 18875 no. surface atoms = 915 nbur = 1373 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 379 mr = 3731 m= 1 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.3600000 number of dielectric boundary points 3154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1855 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7805 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0383506E-09 1.7264499E-08 midg,1,midg; midg,igrid,midg 2.9983692E-08 -2.1898627E-08 1,midg,midg; igrid,midg,midg 3.0029909E-08 -2.1395897E-08 gauss-seidel spectral radius is 0.9880387 estimated iterations to convergence 75 setup time was (sec) 0.6500000 now iterating at: 07:59:57 rms-change max change #iterations 0.1538757 23.09084 at 10iterations 1.6576262E-02 2.261398 at 20iterations 1.7443532E-03 0.2757602 at 30iterations 1.8215788E-04 2.7423859E-02 at 40iterations 1.9433190E-05 2.8800964E-03 at 50iterations finished qdiffx linear iterations at : 08:00:01 total time elapsed so far: 4.540000 # loops : 50 mean,max change (kT/e) : 1.9433190E-05 2.8800964E-03 energy calculations done at 4.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.890000 DelPhi exited at 08:00:02 4.894u 0.388s 0:05.70 92.4% 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 Tue Oct 11 2011 at 08:00:02 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 = 2288 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: 1.977412 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): -57.99000 -3.980000 ymin,ymax (A): 64.01200 108.3240 zmin,zma (A): -24.93200 19.25700 x,y,z range (A): 54.01000 44.31200 44.18900 scale (grids/A): 1.977412 object centre (A): -30.98500 86.16800 -2.837500 number of atom coordinates read : 2288 total number of charged atoms : 2152 net assigned charge : 4.000010 assigned positive charge : 339.7426 centred at (gu) : 93.10253 93.21677 91.49401 assigned negative charge : -335.7429 centred at (gu) : 93.59006 93.70873 91.40405 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 70321 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18875 grid for indexing accessible points = 1.400000 m= 26348 mr = 49354 m= 4504 mr = 19907 m= 289 mr = 2931 m= 8 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 2905 time to turn everything in is 0.7100000 number of dielectric boundary points 29137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 17010 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) : 0.6591372 object centre at (A) : -30.98500 86.16800 -2.837500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9792192E-02 2.2195362E-02 midg,1,midg; midg,igrid,midg 2.2411088E-02 -2.4070073E-02 1,midg,midg; igrid,midg,midg 5.2753929E-02 2.0929959E-02 gauss-seidel spectral radius is 0.9986955 estimated iterations to convergence 219 setup time was (sec) 1.040000 now iterating at: 08:00:03 rms-change max change #iterations 4.149639 186.0983 at 10iterations 1.975916 67.29749 at 20iterations 0.9462140 30.92459 at 30iterations 0.4509022 15.53524 at 40iterations 0.2148538 6.947213 at 50iterations 0.1024609 3.111355 at 60iterations 4.8940104E-02 1.556664 at 70iterations 2.3378862E-02 0.7967048 at 80iterations 1.1116209E-02 0.4027481 at 90iterations 5.2859280E-03 0.1747231 at 100iterations 2.5211747E-03 7.8784943E-02 at 110iterations 1.2091104E-03 3.6706448E-02 at 120iterations finished qdiffx linear iterations at : 08:00:12 total time elapsed so far: 9.940000 # loops : 120 mean,max change (kT/e) : 1.2091104E-03 3.6706448E-02 energy calculations done at 9.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.15000 DelPhi exited at 08:00:12 10.158u 0.465s 0:10.93 97.0% 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 08:00:13 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 = 2288 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: 2.966117 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): -57.99000 -3.980000 ymin,ymax (A): 64.01200 108.3240 zmin,zma (A): -24.93200 19.25700 x,y,z range (A): 54.01000 44.31200 44.18900 scale (grids/A): 2.966117 object centre (A): -30.98500 86.16800 -2.837500 number of atom coordinates read : 2288 total number of charged atoms : 2152 net assigned charge : 4.000010 assigned positive charge : 339.7426 centred at (gu) : 94.65379 94.82506 92.24093 assigned negative charge : -335.7429 centred at (gu) : 95.38508 95.56304 92.10614 start vw surface at 0.1500000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 162305 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18875 grid for indexing accessible points = 1.400000 m= 83741 mr = 118762 m= 32032 mr = 69509 m= 8438 mr = 26406 m= 1259 mr = 6470 m= 140 mr = 870 m= 12 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 9624 time to turn everything in is 1.890000 number of dielectric boundary points 65804 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 17212 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) : 1.977412 object centre at (A) : -30.98500 86.16800 -2.837500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2820048 0.2586559 midg,1,midg; midg,igrid,midg 0.1884274 -0.3588303 1,midg,midg; igrid,midg,midg 0.7071354 0.3472673 gauss-seidel spectral radius is 0.9992607 estimated iterations to convergence 290 setup time was (sec) 2.260000 now iterating at: 08:00:15 rms-change max change #iterations 9.597079 425.3445 at 10iterations 5.556190 155.2670 at 20iterations 3.214398 67.21710 at 30iterations 1.853199 35.67007 at 40iterations 1.069086 19.29226 at 50iterations 0.6151757 11.15305 at 60iterations 0.3543482 6.899012 at 70iterations 0.2038947 3.747070 at 80iterations 0.1173226 2.086518 at 90iterations 6.7423627E-02 1.176262 at 100iterations 3.8812172E-02 0.6875076 at 110iterations 2.2326278E-02 0.3946126 at 120iterations 1.2826586E-02 0.2599487 at 130iterations 7.4021909E-03 0.1324692 at 140iterations 4.2459690E-03 7.6370239E-02 at 150iterations 2.4540031E-03 4.3907166E-02 at 160iterations 1.4160479E-03 2.5424957E-02 at 170iterations 8.2162971E-04 1.7539978E-02 at 180iterations finished qdiffx linear iterations at : 08:00:30 total time elapsed so far: 16.99000 # loops : 180 mean,max change (kT/e) : 8.2162971E-04 1.7539978E-02 energy calculations done at 16.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.20000 DelPhi exited at 08:00:31 17.207u 0.489s 0:18.30 96.6% 0+0k 0+0io 0pf+0w