Sat Oct 8 14:19:15 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 14:19:15 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3044 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 0.6350112 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): -14.47000 35.27000 ymin,ymax (A): -11.67700 44.38500 zmin,zma (A): -39.98600 12.68500 x,y,z range (A): 49.74000 56.06200 52.67100 scale (grids/A): 0.6350112 object centre (A): 10.40000 16.35400 -13.65050 number of atom coordinates read : 3044 total number of charged atoms : 2897 net assigned charge : 1.4008060E-02 assigned positive charge : 457.4666 centred at (gu) : 91.77974 91.97886 91.15810 assigned negative charge : -457.4533 centred at (gu) : 91.83054 91.89415 91.23256 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8100 nv = 96 ne = 84 npr = 63818 no. pairs analyzed = 63818 no. exposed pairs = 3486 no. arc points = 24214 no. surface atoms = 1184 nbur = 1860 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 415 mr = 4730 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3752 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2340 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9885 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8417645E-09 -1.1469811E-08 midg,1,midg; midg,igrid,midg -6.5797776E-09 1.5534223E-08 1,midg,midg; igrid,midg,midg 4.1010111E-09 -8.9520507E-09 gauss-seidel spectral radius is 0.9871849 estimated iterations to convergence 72 setup time was (sec) 0.6000000 now iterating at: 14:19:16 rms-change max change #iterations 0.1602971 19.78488 at 10iterations 1.5983980E-02 2.202530 at 20iterations 1.6564286E-03 0.1922073 at 30iterations 1.9796248E-04 2.5196075E-02 at 40iterations 3.0965628E-05 4.5948029E-03 at 50iterations finished qdiffx linear iterations at : 14:19:20 total time elapsed so far: 4.450000 # loops : 50 mean,max change (kT/e) : 3.0965628E-05 4.5948029E-03 energy calculations done at 4.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 14:19:21 4.619u 0.399s 0:05.39 92.7% 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 14:19:21 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3044 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 1.905034 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): -14.47000 35.27000 ymin,ymax (A): -11.67700 44.38500 zmin,zma (A): -39.98600 12.68500 x,y,z range (A): 49.74000 56.06200 52.67100 scale (grids/A): 1.905034 object centre (A): 10.40000 16.35400 -13.65050 number of atom coordinates read : 3044 total number of charged atoms : 2897 net assigned charge : 1.4008060E-02 assigned positive charge : 457.4666 centred at (gu) : 95.33892 95.93549 93.47388 assigned negative charge : -457.4533 centred at (gu) : 95.49142 95.68217 93.69739 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 88331 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24214 grid for indexing accessible points = 1.400000 m= 32028 mr = 63744 m= 4663 mr = 24070 m= 227 mr = 2869 m= 8 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 220 time to turn everything in is 0.7000000 number of dielectric boundary points 34516 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 163 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 22807 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) : 0.6350112 object centre at (A) : 10.40000 16.35400 -13.65050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7969549E-02 9.0436563E-03 midg,1,midg; midg,igrid,midg -2.5048148E-02 5.3757608E-02 1,midg,midg; igrid,midg,midg 8.4791416E-03 -1.8152656E-02 gauss-seidel spectral radius is 0.9986677 estimated iterations to convergence 217 setup time was (sec) 1.040000 now iterating at: 14:19:22 rms-change max change #iterations 4.724038 197.7775 at 10iterations 2.237508 69.90901 at 20iterations 1.060404 31.41819 at 30iterations 0.5020649 16.32372 at 40iterations 0.2383961 6.595359 at 50iterations 0.1127896 3.537522 at 60iterations 5.3435087E-02 1.576336 at 70iterations 2.5254495E-02 0.7729249 at 80iterations 1.1983879E-02 0.3244505 at 90iterations 5.6841047E-03 0.1564541 at 100iterations 2.6986934E-03 7.6913118E-02 at 110iterations 1.2845485E-03 3.5701752E-02 at 120iterations finished qdiffx linear iterations at : 14:19:32 total time elapsed so far: 10.58000 # loops : 120 mean,max change (kT/e) : 1.2845485E-03 3.5701752E-02 energy calculations done at 10.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.75000 DelPhi exited at 14:19:32 10.750u 0.438s 0:11.50 97.2% 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 14:19:32 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3044 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 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: 2.857550 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): -14.47000 35.27000 ymin,ymax (A): -11.67700 44.38500 zmin,zma (A): -39.98600 12.68500 x,y,z range (A): 49.74000 56.06200 52.67100 scale (grids/A): 2.857550 object centre (A): 10.40000 16.35400 -13.65050 number of atom coordinates read : 3044 total number of charged atoms : 2897 net assigned charge : 1.4008060E-02 assigned positive charge : 457.4666 centred at (gu) : 98.00811 98.90294 95.21073 assigned negative charge : -457.4533 centred at (gu) : 98.23694 98.52325 95.54599 start vw surface at 0.1400000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 204774 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24214 grid for indexing accessible points = 1.400000 m= 105261 mr = 154421 m= 36914 mr = 87473 m= 8265 mr = 29865 m= 1101 mr = 6096 m= 61 mr = 686 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 874 time to turn everything in is 1.890000 number of dielectric boundary points 77814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 23175 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) : 1.905034 object centre at (A) : 10.40000 16.35400 -13.65050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1572186 0.2918361 midg,1,midg; midg,igrid,midg -0.1893607 0.7171154 1,midg,midg; igrid,midg,midg 0.1147535 -0.1265954 gauss-seidel spectral radius is 0.9992714 estimated iterations to convergence 292 setup time was (sec) 2.230000 now iterating at: 14:19:35 rms-change max change #iterations 10.94367 415.8678 at 10iterations 6.414681 124.0523 at 20iterations 3.736643 73.78976 at 30iterations 2.177600 38.25017 at 40iterations 1.264794 27.49660 at 50iterations 0.7325627 14.72808 at 60iterations 0.4247433 7.116954 at 70iterations 0.2457399 3.905277 at 80iterations 0.1422577 2.260334 at 90iterations 8.2329936E-02 1.342676 at 100iterations 4.7639295E-02 0.7886696 at 110iterations 2.7547019E-02 0.4626541 at 120iterations 1.5892955E-02 0.2626324 at 130iterations 9.2219329E-03 0.1446724 at 140iterations 5.3303805E-03 0.1052704 at 150iterations 3.0904405E-03 4.9324036E-02 at 160iterations 1.7924344E-03 3.5083771E-02 at 170iterations 1.0451358E-03 1.7309189E-02 at 180iterations finished qdiffx linear iterations at : 14:19:51 total time elapsed so far: 18.67000 # loops : 180 mean,max change (kT/e) : 1.0451358E-03 1.7309189E-02 energy calculations done at 18.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.83000 DelPhi exited at 14:19:52 18.835u 0.454s 0:19.58 98.4% 0+0k 0+0io 0pf+0w