Sat Oct 8 22:38:48 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 Sat Oct 8 2011 at 22:38:49 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3211 !!! WARNING: HIT 85 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5958757 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): -15.81100 41.91300 ymin,ymax (A): 16.64500 76.38900 zmin,zma (A): 25.33000 82.99500 x,y,z range (A): 57.72400 59.74400 57.66499 scale (grids/A): 0.5958757 object centre (A): 13.05100 46.51700 54.16250 number of atom coordinates read : 3211 total number of charged atoms : 3070 net assigned charge : 12.24003 assigned positive charge : 475.3758 centred at (gu) : 89.27101 90.03893 91.67708 assigned negative charge : -463.1374 centred at (gu) : 89.10329 90.10809 91.90626 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7736 nv = 96 ne = 84 npr = 62999 no. pairs analyzed = 62999 no. exposed pairs = 4288 no. arc points = 30539 no. surface atoms = 1427 nbur = 1784 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 385 mr = 3985 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3300000 number of dielectric boundary points 4105 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3094 ## 309 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9722 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1046246E-09 -6.3266015E-09 midg,1,midg; midg,igrid,midg 7.3496089E-09 2.1615356E-09 1,midg,midg; igrid,midg,midg -2.0832511E-09 9.3818224E-09 gauss-seidel spectral radius is 0.9854900 estimated iterations to convergence 68 setup time was (sec) 0.5800000 now iterating at: 22:38:49 rms-change max change #iterations 0.1192655 15.66652 at 10iterations 9.9384487E-03 1.367756 at 20iterations 8.4459066E-04 0.1138420 at 30iterations 7.9819474E-05 1.2129784E-02 at 40iterations 9.3292965E-06 1.2159348E-03 at 50iterations finished qdiffx linear iterations at : 22:38:52 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 9.3292965E-06 1.2159348E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 22:38:53 3.554u 0.248s 0:04.17 90.8% 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 Sat Oct 8 2011 at 22:38:53 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3211 !!! WARNING: HIT 85 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.787627 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): -15.81100 41.91300 ymin,ymax (A): 16.64500 76.38900 zmin,zma (A): 25.33000 82.99500 x,y,z range (A): 57.72400 59.74400 57.66499 scale (grids/A): 1.787627 object centre (A): 13.05100 46.51700 54.16250 number of atom coordinates read : 3211 total number of charged atoms : 3070 net assigned charge : 12.24003 assigned positive charge : 475.3758 centred at (gu) : 87.81239 90.11642 95.03026 assigned negative charge : -463.1374 centred at (gu) : 87.30967 90.32453 95.71842 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83849 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30539 grid for indexing accessible points = 1.400000 m= 29071 mr = 55977 m= 4194 mr = 20644 m= 177 mr = 2383 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1791 time to turn everything in is 0.6000000 number of dielectric boundary points 38251 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 239 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 23946 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) : 0.5958757 object centre at (A) : 13.05100 46.51700 54.16250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7927842E-02 5.2337046E-03 midg,1,midg; midg,igrid,midg 4.9850605E-02 2.1442099E-02 1,midg,midg; igrid,midg,midg -6.5488485E-03 3.6244381E-02 gauss-seidel spectral radius is 0.9985296 estimated iterations to convergence 207 setup time was (sec) 0.9200000 now iterating at: 22:38:54 rms-change max change #iterations 4.162382 172.9770 at 10iterations 1.876804 60.07595 at 20iterations 0.8548876 26.78773 at 30iterations 0.3887292 11.84346 at 40iterations 0.1761086 5.635692 at 50iterations 7.9813488E-02 2.410290 at 60iterations 3.6362112E-02 1.197552 at 70iterations 1.6529225E-02 0.4864845 at 80iterations 7.5220754E-03 0.2393475 at 90iterations 3.4347815E-03 0.1083460 at 100iterations 1.5583988E-03 4.9973272E-02 at 110iterations 7.0560654E-04 2.2342205E-02 at 120iterations finished qdiffx linear iterations at : 22:39:01 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 7.0560654E-04 2.2342205E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 22:39:01 8.170u 0.267s 0:08.76 96.2% 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 Sat Oct 8 2011 at 22:39:02 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3211 !!! WARNING: HIT 85 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.681441 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): -15.81100 41.91300 ymin,ymax (A): 16.64500 76.38900 zmin,zma (A): 25.33000 82.99500 x,y,z range (A): 57.72400 59.74400 57.66499 scale (grids/A): 2.681441 object centre (A): 13.05100 46.51700 54.16250 number of atom coordinates read : 3211 total number of charged atoms : 3070 net assigned charge : 12.24003 assigned positive charge : 475.3758 centred at (gu) : 86.71816 90.17432 97.54501 assigned negative charge : -463.1374 centred at (gu) : 85.96449 90.48668 98.57779 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 194154 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30539 grid for indexing accessible points = 1.400000 m= 94387 mr = 136693 m= 32761 mr = 75202 m= 7067 mr = 25509 m= 769 mr = 4959 m= 28 mr = 446 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.8500001 no. cavity mid-points inaccessible to solvent = 6186 time to turn everything in is 1.470000 number of dielectric boundary points 86358 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 24535 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) : 1.787627 object centre at (A) : 13.05100 46.51700 54.16250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6650910 0.1425580 midg,1,midg; midg,igrid,midg 0.6529669 0.5350326 1,midg,midg; igrid,midg,midg 1.0254284E-02 0.5862642 gauss-seidel spectral radius is 0.9992592 estimated iterations to convergence 290 setup time was (sec) 1.810000 now iterating at: 22:39:04 rms-change max change #iterations 10.30237 373.9677 at 10iterations 6.080700 156.3931 at 20iterations 3.562328 81.16991 at 30iterations 2.078540 42.85337 at 40iterations 1.208663 22.61009 at 50iterations 0.6988036 13.97372 at 60iterations 0.4043487 8.296378 at 70iterations 0.2331659 4.339975 at 80iterations 0.1345888 2.372784 at 90iterations 7.7484041E-02 1.511952 at 100iterations 4.4534683E-02 0.8431320 at 110iterations 2.5629483E-02 0.4491777 at 120iterations 1.4724145E-02 0.2852912 at 130iterations 8.4694615E-03 0.1518145 at 140iterations 4.8681591E-03 0.1080360 at 150iterations 2.7986676E-03 5.0765991E-02 at 160iterations 1.6045165E-03 2.8999329E-02 at 170iterations 9.2048297E-04 1.6067505E-02 at 180iterations finished qdiffx linear iterations at : 22:39:15 total time elapsed so far: 13.44000 # loops : 180 mean,max change (kT/e) : 9.2048297E-04 1.6067505E-02 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.61000 DelPhi exited at 22:39:16 13.615u 0.295s 0:14.19 97.9% 0+0k 0+0io 0pf+0w