Mon Oct 10 09:44:34 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 09:44:34 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 = 2739 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: 0.6011686 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): -16.80100 36.31600 ymin,ymax (A): -64.12800 -4.910000 zmin,zma (A): -3.916000 48.77400 x,y,z range (A): 53.11700 59.21800 52.69000 scale (grids/A): 0.6011686 object centre (A): 9.757499 -34.51900 22.42900 number of atom coordinates read : 2739 total number of charged atoms : 2589 net assigned charge : 2.000010 assigned positive charge : 398.7272 centred at (gu) : 88.88406 89.48544 89.67790 assigned negative charge : -396.7274 centred at (gu) : 89.02016 89.41509 89.62660 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6726 nv = 96 ne = 84 npr = 53690 no. pairs analyzed = 53690 no. exposed pairs = 4200 no. arc points = 30461 no. surface atoms = 1376 nbur = 1363 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 2983 m= 3 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 4097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2920 ## 281 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8277 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2345963E-09 2.6229066E-09 midg,1,midg; midg,igrid,midg -2.1343987E-09 3.1560317E-09 1,midg,midg; igrid,midg,midg 7.7972846E-09 -3.4669601E-09 gauss-seidel spectral radius is 0.9857092 estimated iterations to convergence 69 setup time was (sec) 0.4100000 now iterating at: 09:44:34 rms-change max change #iterations 0.1079329 20.34278 at 10iterations 9.1230655E-03 1.489084 at 20iterations 7.5859873E-04 0.1184826 at 30iterations 6.9419664E-05 1.2374878E-02 at 40iterations 8.4294797E-06 1.1055470E-03 at 50iterations finished qdiffx linear iterations at : 09:44:37 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 8.4294797E-06 1.1055470E-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 09:44:38 3.457u 0.164s 0:04.01 90.0% 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 09:44:38 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 = 2739 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: 1.803506 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): -16.80100 36.31600 ymin,ymax (A): -64.12800 -4.910000 zmin,zma (A): -3.916000 48.77400 x,y,z range (A): 53.11700 59.21800 52.69000 scale (grids/A): 1.803506 object centre (A): 9.757499 -34.51900 22.42900 number of atom coordinates read : 2739 total number of charged atoms : 2589 net assigned charge : 2.000010 assigned positive charge : 398.7272 centred at (gu) : 86.65196 88.45574 89.03355 assigned negative charge : -396.7274 centred at (gu) : 87.06022 88.24506 88.87971 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71324 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30461 grid for indexing accessible points = 1.400000 m= 23380 mr = 43758 m= 3277 mr = 14702 m= 143 mr = 1494 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 97 time to turn everything in is 0.3600000 number of dielectric boundary points 38154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 234 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 20230 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) : 0.6011686 object centre at (A) : 9.757499 -34.51900 22.42900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6973680E-04 -5.1394952E-03 midg,1,midg; midg,igrid,midg 2.0497024E-02 3.6481902E-02 1,midg,midg; igrid,midg,midg 2.0476837E-02 -7.4164849E-03 gauss-seidel spectral radius is 0.9985213 estimated iterations to convergence 206 setup time was (sec) 0.5900000 now iterating at: 09:44:39 rms-change max change #iterations 3.848620 242.1248 at 10iterations 1.738076 68.72433 at 20iterations 0.7877217 26.70168 at 30iterations 0.3565222 13.00678 at 40iterations 0.1617389 5.724986 at 50iterations 7.3391899E-02 2.440784 at 60iterations 3.3201527E-02 1.300926 at 70iterations 1.5091051E-02 0.5184736 at 80iterations 6.8511427E-03 0.2359772 at 90iterations 3.1046108E-03 0.1061172 at 100iterations 1.4089565E-03 4.4938087E-02 at 110iterations 6.3773274E-04 2.4953842E-02 at 120iterations finished qdiffx linear iterations at : 09:44:46 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 6.3773274E-04 2.4953842E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 09:44:46 7.930u 0.203s 0:08.41 96.6% 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 09:44:46 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 = 2739 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: 2.705259 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): -16.80100 36.31600 ymin,ymax (A): -64.12800 -4.910000 zmin,zma (A): -3.916000 48.77400 x,y,z range (A): 53.11700 59.21800 52.69000 scale (grids/A): 2.705259 object centre (A): 9.757499 -34.51900 22.42900 number of atom coordinates read : 2739 total number of charged atoms : 2589 net assigned charge : 2.000010 assigned positive charge : 398.7272 centred at (gu) : 84.97779 87.68372 88.55015 assigned negative charge : -396.7274 centred at (gu) : 85.59026 87.36744 88.31946 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 164637 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30461 grid for indexing accessible points = 1.400000 m= 75168 mr = 107634 m= 25853 mr = 55899 m= 5280 mr = 18487 m= 543 mr = 3131 m= 25 mr = 206 m= 0 mr = 3 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 408 time to turn everything in is 0.9400000 number of dielectric boundary points 86146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 20711 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) : 1.803506 object centre at (A) : 9.757499 -34.51900 22.42900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9876951E-02 -5.5400852E-02 midg,1,midg; midg,igrid,midg 0.4280145 0.5252460 1,midg,midg; igrid,midg,midg 0.1991124 -4.1260920E-02 gauss-seidel spectral radius is 0.9992580 estimated iterations to convergence 290 setup time was (sec) 1.170000 now iterating at: 09:44:48 rms-change max change #iterations 9.624119 337.4859 at 10iterations 5.748201 156.7701 at 20iterations 3.387986 81.77614 at 30iterations 1.988452 48.53841 at 40iterations 1.160407 28.54091 at 50iterations 0.6734462 15.22148 at 60iterations 0.3911329 8.640152 at 70iterations 0.2255122 5.589043 at 80iterations 0.1307301 3.127492 at 90iterations 7.5617366E-02 1.844261 at 100iterations 4.3587334E-02 0.9503732 at 110iterations 2.5101641E-02 0.5538464 at 120iterations 1.4458948E-02 0.2987175 at 130iterations 8.3102817E-03 0.1662445 at 140iterations 4.7758203E-03 9.6335411E-02 at 150iterations 2.7407291E-03 5.4351807E-02 at 160iterations 1.5764558E-03 3.4656167E-02 at 170iterations 9.0700708E-04 2.2547722E-02 at 180iterations finished qdiffx linear iterations at : 09:44:59 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 9.0700708E-04 2.2547722E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 09:45:00 12.821u 0.214s 0:13.45 96.8% 0+0k 0+0io 0pf+0w