Mon Oct 10 14:10:48 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+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 14:10:48 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 = 3383 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.6164609 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): 35.34700 85.18400 ymin,ymax (A): 26.23500 83.98400 zmin,zma (A): -3.295000 45.73100 x,y,z range (A): 49.83700 57.74900 49.02600 scale (grids/A): 0.6164609 object centre (A): 60.26550 55.10950 21.21800 number of atom coordinates read : 3383 total number of charged atoms : 3249 net assigned charge : -6.499967 assigned positive charge : 517.3441 centred at (gu) : 91.20515 89.56083 90.76428 assigned negative charge : -523.8453 centred at (gu) : 91.03928 89.62070 90.78953 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8337 nv = 96 ne = 84 npr = 71103 no. pairs analyzed = 71103 no. exposed pairs = 3761 no. arc points = 25624 no. surface atoms = 1283 nbur = 2100 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 470 mr = 5000 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 118 time to turn everything in is 0.3800000 number of dielectric boundary points 3747 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2531 ## 230 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10436 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4141966E-09 -8.1601570E-09 midg,1,midg; midg,igrid,midg -3.1910596E-11 -8.8346468E-09 1,midg,midg; igrid,midg,midg -1.4179496E-08 1.0994688E-08 gauss-seidel spectral radius is 0.9864298 estimated iterations to convergence 70 setup time was (sec) 0.6000000 now iterating at: 14:10:48 rms-change max change #iterations 0.1483439 22.86601 at 10iterations 1.3517637E-02 1.695452 at 20iterations 1.3476264E-03 0.1673479 at 30iterations 1.9506957E-04 3.3305168E-02 at 40iterations 4.9496593E-05 9.3841553E-03 at 50iterations finished qdiffx linear iterations at : 14:10:51 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 4.9496593E-05 9.3841553E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 14:10:52 3.443u 0.190s 0:04.22 86.0% 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 14:10:52 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 = 3383 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: 1.849383 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): 35.34700 85.18400 ymin,ymax (A): 26.23500 83.98400 zmin,zma (A): -3.295000 45.73100 x,y,z range (A): 49.83700 57.74900 49.02600 scale (grids/A): 1.849383 object centre (A): 60.26550 55.10950 21.21800 number of atom coordinates read : 3383 total number of charged atoms : 3249 net assigned charge : -6.499967 assigned positive charge : 517.3441 centred at (gu) : 93.61443 88.68168 92.29176 assigned negative charge : -523.8453 centred at (gu) : 93.11726 88.86127 92.36797 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 89190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25624 grid for indexing accessible points = 1.400000 m= 36368 mr = 64642 m= 6439 mr = 28693 m= 291 mr = 4381 m= 1 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 4422 time to turn everything in is 0.6500000 number of dielectric boundary points 34498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 25475 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) : 0.6164609 object centre at (A) : 60.26550 55.10950 21.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8424880E-02 -2.6336834E-02 midg,1,midg; midg,igrid,midg 2.7731298E-03 -4.0161815E-02 1,midg,midg; igrid,midg,midg -2.8936477E-02 1.8631849E-02 gauss-seidel spectral radius is 0.9986158 estimated iterations to convergence 213 setup time was (sec) 0.9300000 now iterating at: 14:10:53 rms-change max change #iterations 4.725053 167.2113 at 10iterations 2.206469 76.62459 at 20iterations 1.027723 29.30474 at 30iterations 0.4790902 13.42327 at 40iterations 0.2242890 7.309052 at 50iterations 0.1049702 2.833376 at 60iterations 4.8778936E-02 1.390860 at 70iterations 2.2833407E-02 0.6579132 at 80iterations 1.0682269E-02 0.3041468 at 90iterations 5.0088759E-03 0.1498184 at 100iterations 2.3614611E-03 7.4495316E-02 at 110iterations 1.1208889E-03 3.2859802E-02 at 120iterations finished qdiffx linear iterations at : 14:11:00 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.1208889E-03 3.2859802E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 14:11:01 7.760u 0.224s 0:08.63 92.4% 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 14:11:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3383 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.774074 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): 35.34700 85.18400 ymin,ymax (A): 26.23500 83.98400 zmin,zma (A): -3.295000 45.73100 x,y,z range (A): 49.83700 57.74900 49.02600 scale (grids/A): 2.774074 object centre (A): 60.26550 55.10950 21.21800 number of atom coordinates read : 3383 total number of charged atoms : 3249 net assigned charge : -6.499967 assigned positive charge : 517.3441 centred at (gu) : 95.42135 88.02224 93.43755 assigned negative charge : -523.8453 centred at (gu) : 94.67566 88.29174 93.55180 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 206215 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25624 grid for indexing accessible points = 1.400000 m= 112544 mr = 155400 m= 46836 mr = 95363 m= 11866 mr = 40017 m= 1378 mr = 9397 m= 56 mr = 855 m= 0 mr = 20 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 15135 time to turn everything in is 1.620000 number of dielectric boundary points 77843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 25990 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) : 1.849383 object centre at (A) : 60.26550 55.10950 21.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2750830 -0.2943641 midg,1,midg; midg,igrid,midg -0.1402600 -0.2777236 1,midg,midg; igrid,midg,midg -0.2768400 0.2459776 gauss-seidel spectral radius is 0.9992593 estimated iterations to convergence 290 setup time was (sec) 1.950000 now iterating at: 14:11:03 rms-change max change #iterations 11.10806 344.1439 at 10iterations 6.488044 159.2021 at 20iterations 3.769641 99.16866 at 30iterations 2.186339 40.19628 at 40iterations 1.267622 27.93443 at 50iterations 0.7321382 13.33290 at 60iterations 0.4222823 7.118395 at 70iterations 0.2431136 4.663467 at 80iterations 0.1403871 2.381568 at 90iterations 8.0650836E-02 1.313021 at 100iterations 4.6506654E-02 0.7439423 at 110iterations 2.6805256E-02 0.4490395 at 120iterations 1.5444910E-02 0.2760735 at 130iterations 8.9393873E-03 0.1555290 at 140iterations 5.1910942E-03 8.6126328E-02 at 150iterations 3.0307348E-03 5.0680399E-02 at 160iterations 1.7968328E-03 3.2828331E-02 at 170iterations 1.0887739E-03 2.0330906E-02 at 180iterations finished qdiffx linear iterations at : 14:11:14 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 1.0887739E-03 2.0330906E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 14:11:14 12.879u 0.223s 0:13.46 97.2% 0+0k 0+0io 0pf+0w