Tue Oct 11 08:10:27 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 08:10:27 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1227 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: ZN2 203 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7422853 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): 12.79100 51.66000 ymin,ymax (A): -32.46000 11.70400 zmin,zma (A): -23.66100 24.29900 x,y,z range (A): 38.86900 44.16400 47.96000 scale (grids/A): 0.7422853 object centre (A): 32.22550 -10.37800 0.3190002 number of atom coordinates read : 1227 total number of charged atoms : 1139 net assigned charge : 0.6000057 assigned positive charge : 182.0161 centred at (gu) : 90.14391 87.88805 91.90630 assigned negative charge : -181.4162 centred at (gu) : 90.00819 87.96398 91.75993 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4782 nv = 96 ne = 84 npr = 23345 no. pairs analyzed = 23345 no. exposed pairs = 1846 no. arc points = 13505 no. surface atoms = 616 nbur = 611 mkacc time = 5.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 322 mr = 2186 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 5.0000012E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1062 ## 73 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 4842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.6147936E-08 1.3636618E-07 midg,1,midg; midg,igrid,midg 7.9770111E-08 -2.5116536E-08 1,midg,midg; igrid,midg,midg -7.2220338E-08 9.0774506E-08 gauss-seidel spectral radius is 0.9904596 estimated iterations to convergence 83 setup time was (sec) 0.4200000 now iterating at: 08:10:27 rms-change max change #iterations 0.1877958 35.78916 at 10iterations 2.4577644E-02 4.348995 at 20iterations 3.2613864E-03 0.5535202 at 30iterations 4.3338907E-04 7.8186989E-02 at 40iterations 5.6592540E-05 9.4809532E-03 at 50iterations finished qdiffx linear iterations at : 08:10:30 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 5.6592540E-05 9.4809532E-03 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 08:10:31 3.244u 0.146s 0:03.95 85.5% 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 08:10:31 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1227 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: ZN2 203 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.226856 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): 12.79100 51.66000 ymin,ymax (A): -32.46000 11.70400 zmin,zma (A): -23.66100 24.29900 x,y,z range (A): 38.86900 44.16400 47.96000 scale (grids/A): 2.226856 object centre (A): 32.22550 -10.37800 0.3190002 number of atom coordinates read : 1227 total number of charged atoms : 1139 net assigned charge : 0.6000057 assigned positive charge : 182.0161 centred at (gu) : 90.43184 83.66431 95.71924 assigned negative charge : -181.4162 centred at (gu) : 90.02479 83.89211 95.28009 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 49436 reading accessible surface arcs data from file ARCDAT no. of arc points read = 13505 grid for indexing accessible points = 1.400000 m= 17221 mr = 30348 m= 3417 mr = 11668 m= 293 mr = 1886 m= 13 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 26402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9068 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) : 0.7422853 object centre at (A) : 32.22550 -10.37800 0.3190002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8681383E-04 1.0994120E-02 midg,1,midg; midg,igrid,midg -1.0749094E-02 -1.1385149E-02 1,midg,midg; igrid,midg,midg 2.0714079E-03 1.7273664E-02 gauss-seidel spectral radius is 0.9988530 estimated iterations to convergence 234 setup time was (sec) 0.7300000 now iterating at: 08:10:32 rms-change max change #iterations 3.765744 220.5839 at 10iterations 1.862590 79.72478 at 20iterations 0.9293525 38.06092 at 30iterations 0.4606969 17.33630 at 40iterations 0.2274954 9.580688 at 50iterations 0.1129404 4.387440 at 60iterations 5.6031331E-02 2.076333 at 70iterations 2.7899254E-02 0.9561768 at 80iterations 1.3745724E-02 0.4922867 at 90iterations 6.8769944E-03 0.2851753 at 100iterations 3.3993472E-03 0.1162758 at 110iterations 1.6858221E-03 6.6879272E-02 at 120iterations finished qdiffx linear iterations at : 08:10:39 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 1.6858221E-03 6.6879272E-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) 7.970000 DelPhi exited at 08:10:39 7.976u 0.210s 0:08.59 95.2% 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 Tue Oct 11 2011 at 08:10:39 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1227 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: ZN2 203 has a net charge of 1.4000 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: 3.340284 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): 12.79100 51.66000 ymin,ymax (A): -32.46000 11.70400 zmin,zma (A): -23.66100 24.29900 x,y,z range (A): 38.86900 44.16400 47.96000 scale (grids/A): 3.340284 object centre (A): 32.22550 -10.37800 0.3190002 number of atom coordinates read : 1227 total number of charged atoms : 1139 net assigned charge : 0.6000057 assigned positive charge : 182.0161 centred at (gu) : 90.64780 80.49648 98.57879 assigned negative charge : -181.4162 centred at (gu) : 90.03727 80.83814 97.92028 start vw surface at 0.1300000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 113530 reading accessible surface arcs data from file ARCDAT no. of arc points read = 13505 grid for indexing accessible points = 1.400000 m= 53700 mr = 73908 m= 21020 mr = 41528 m= 6162 mr = 15912 m= 1170 mr = 4261 m= 96 mr = 594 m= 0 mr = 29 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 59446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 9112 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) : 2.226856 object centre at (A) : 32.22550 -10.37800 0.3190002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0063600E-02 9.2163660E-02 midg,1,midg; midg,igrid,midg -6.1898665E-03 -0.1060054 1,midg,midg; igrid,midg,midg 4.1613422E-02 0.1166833 gauss-seidel spectral radius is 0.9993196 estimated iterations to convergence 302 setup time was (sec) 1.560000 now iterating at: 08:10:41 rms-change max change #iterations 8.390011 291.5839 at 10iterations 4.986020 126.1741 at 20iterations 2.947947 65.27604 at 30iterations 1.732086 39.01413 at 40iterations 1.016323 22.63693 at 50iterations 0.5965342 14.43901 at 60iterations 0.3497378 7.332697 at 70iterations 0.2051824 4.400223 at 80iterations 0.1197563 2.491421 at 90iterations 7.0138603E-02 1.524063 at 100iterations 4.1109920E-02 0.8366199 at 110iterations 2.4040727E-02 0.5055442 at 120iterations 1.4088278E-02 0.3016300 at 130iterations 8.2315318E-03 0.1750603 at 140iterations 4.8230556E-03 0.1023064 at 150iterations 2.8258464E-03 6.5263748E-02 at 160iterations 1.6567988E-03 3.3205032E-02 at 170iterations 9.6842484E-04 2.0874023E-02 at 180iterations finished qdiffx linear iterations at : 08:10:52 total time elapsed so far: 12.33000 # loops : 180 mean,max change (kT/e) : 9.6842484E-04 2.0874023E-02 energy calculations done at 12.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 08:10:53 12.511u 0.190s 0:13.21 96.1% 0+0k 0+0io 0pf+0w