Tue Oct 11 07:51:41 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 Tue Oct 11 2011 at 07:51:41 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2376 !!! WARNING: HIR 54 has a net charge of 0.5140 !!! WARNING: HIR 106 has a net charge of 0.5140 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: GLM 208 has a net charge of -0.0940 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: 0.6435286 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): -9.067000 39.67500 ymin,ymax (A): -14.41300 40.90700 zmin,zma (A): 5.085000 52.57700 x,y,z range (A): 48.74200 55.32000 47.49200 scale (grids/A): 0.6435286 object centre (A): 15.30400 13.24700 28.83100 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 3.959009 assigned positive charge : 357.5483 centred at (gu) : 89.51910 88.59457 90.63780 assigned negative charge : -353.5898 centred at (gu) : 89.43340 88.61301 90.80761 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6667 nv = 96 ne = 84 npr = 47978 no. pairs analyzed = 47978 no. exposed pairs = 2848 no. arc points = 19996 no. surface atoms = 967 nbur = 1409 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 385 mr = 3766 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2050 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7860 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2679501E-08 -1.5720047E-08 midg,1,midg; midg,igrid,midg 1.1678562E-08 3.3213070E-09 1,midg,midg; igrid,midg,midg -3.9768162E-09 1.4852481E-08 gauss-seidel spectral radius is 0.9874687 estimated iterations to convergence 73 setup time was (sec) 0.5800000 now iterating at: 07:51:42 rms-change max change #iterations 0.1443289 21.69833 at 10iterations 1.5078654E-02 1.999350 at 20iterations 1.6671610E-03 0.2909393 at 30iterations 2.2426534E-04 3.6834717E-02 at 40iterations 3.8363247E-05 6.6871643E-03 at 50iterations finished qdiffx linear iterations at : 07:51:46 total time elapsed so far: 4.300000 # loops : 50 mean,max change (kT/e) : 3.8363247E-05 6.6871643E-03 energy calculations done at 4.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 07:51:47 4.467u 0.389s 0:05.62 86.1% 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 07:51:47 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2376 !!! WARNING: HIR 54 has a net charge of 0.5140 !!! WARNING: HIR 106 has a net charge of 0.5140 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: GLM 208 has a net charge of -0.0940 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: 1.930586 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): -9.067000 39.67500 ymin,ymax (A): -14.41300 40.90700 zmin,zma (A): 5.085000 52.57700 x,y,z range (A): 48.74200 55.32000 47.49200 scale (grids/A): 1.930586 object centre (A): 15.30400 13.24700 28.83100 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 3.959009 assigned positive charge : 357.5483 centred at (gu) : 88.55709 85.78336 91.91327 assigned negative charge : -353.5898 centred at (gu) : 88.30010 85.83889 92.42268 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 71879 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19996 grid for indexing accessible points = 1.400000 m= 27457 mr = 50525 m= 4295 mr = 20737 m= 291 mr = 2839 m= 7 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1217 time to turn everything in is 0.5900000 number of dielectric boundary points 29715 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 166 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 17611 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) : 0.6435286 object centre at (A) : 15.30400 13.24700 28.83100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1001990E-02 -2.3318868E-02 midg,1,midg; midg,igrid,midg 3.0166328E-02 1.8597111E-02 1,midg,midg; igrid,midg,midg -4.4632442E-03 4.7428180E-03 gauss-seidel spectral radius is 0.9986479 estimated iterations to convergence 215 setup time was (sec) 0.9300000 now iterating at: 07:51:48 rms-change max change #iterations 4.082640 165.1731 at 10iterations 1.916452 73.58476 at 20iterations 0.9066036 29.82586 at 30iterations 0.4276701 13.31890 at 40iterations 0.2009877 6.770500 at 50iterations 9.4578378E-02 3.060340 at 60iterations 4.4684265E-02 1.468987 at 70iterations 2.1082964E-02 0.6895428 at 80iterations 9.9295257E-03 0.3246536 at 90iterations 4.7057485E-03 0.1426036 at 100iterations 2.2243888E-03 7.3150635E-02 at 110iterations 1.0575906E-03 3.6231995E-02 at 120iterations finished qdiffx linear iterations at : 07:51:57 total time elapsed so far: 10.39000 # loops : 120 mean,max change (kT/e) : 1.0575906E-03 3.6231995E-02 energy calculations done at 10.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.56000 DelPhi exited at 07:51:59 10.564u 0.445s 0:12.30 89.4% 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 Tue Oct 11 2011 at 07:51:59 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2376 !!! WARNING: HIR 54 has a net charge of 0.5140 !!! WARNING: HIR 106 has a net charge of 0.5140 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: GLM 208 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.895879 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): -9.067000 39.67500 ymin,ymax (A): -14.41300 40.90700 zmin,zma (A): 5.085000 52.57700 x,y,z range (A): 48.74200 55.32000 47.49200 scale (grids/A): 2.895879 object centre (A): 15.30400 13.24700 28.83100 number of atom coordinates read : 2376 total number of charged atoms : 2234 net assigned charge : 3.959009 assigned positive charge : 357.5483 centred at (gu) : 87.83565 83.67493 92.86988 assigned negative charge : -353.5898 centred at (gu) : 87.45018 83.75835 93.63400 start vw surface at 0.1200000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 165991 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19996 grid for indexing accessible points = 1.400000 m= 87717 mr = 121788 m= 32771 mr = 73048 m= 7821 mr = 26834 m= 1237 mr = 5941 m= 83 mr = 931 m= 0 mr = 38 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 4301 time to turn everything in is 1.560000 number of dielectric boundary points 67040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 17868 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) : 1.930586 object centre at (A) : 15.30400 13.24700 28.83100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4752740 -0.3720135 midg,1,midg; midg,igrid,midg 0.2495995 0.1779352 1,midg,midg; igrid,midg,midg -3.4858733E-02 -2.6725788E-02 gauss-seidel spectral radius is 0.9992541 estimated iterations to convergence 289 setup time was (sec) 1.890000 now iterating at: 07:52:01 rms-change max change #iterations 9.633986 369.7734 at 10iterations 5.611249 150.7109 at 20iterations 3.255635 80.08022 at 30iterations 1.882009 41.10027 at 40iterations 1.084550 21.08026 at 50iterations 0.6256174 12.60736 at 60iterations 0.3604623 7.862813 at 70iterations 0.2068804 4.169540 at 80iterations 0.1189491 2.449432 at 90iterations 6.8463244E-02 1.262056 at 100iterations 3.9284591E-02 0.6998348 at 110iterations 2.2646930E-02 0.4474030 at 120iterations 1.3005681E-02 0.2437506 at 130iterations 7.5027463E-03 0.1384926 at 140iterations 4.3445528E-03 7.8079224E-02 at 150iterations 2.5344428E-03 4.8282623E-02 at 160iterations 1.4935960E-03 2.7462006E-02 at 170iterations 8.9612609E-04 1.7997742E-02 at 180iterations finished qdiffx linear iterations at : 07:52:17 total time elapsed so far: 18.00000 # loops : 180 mean,max change (kT/e) : 8.9612609E-04 1.7997742E-02 energy calculations done at 18.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.17000 DelPhi exited at 07:52:18 18.171u 0.455s 0:18.96 98.2% 0+0k 0+0io 0pf+0w