Tue Oct 11 03:40:11 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 03:40:11 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 = 2765 !!! WARNING: ASP 288 has a net charge of -0.7280 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: 0.6493270 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): 10.35200 65.17800 ymin,ymax (A): -5.452000 47.37900 zmin,zma (A): -6.719000 46.52800 x,y,z range (A): 54.82600 52.83100 53.24700 scale (grids/A): 0.6493270 object centre (A): 37.76500 20.96350 19.90450 number of atom coordinates read : 2765 total number of charged atoms : 2617 net assigned charge : 3.772014 assigned positive charge : 420.1437 centred at (gu) : 91.94914 90.39472 90.51015 assigned negative charge : -416.3723 centred at (gu) : 91.74249 90.56168 90.55795 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7830 nv = 96 ne = 84 npr = 55814 no. pairs analyzed = 55814 no. exposed pairs = 3400 no. arc points = 23977 no. surface atoms = 1140 nbur = 1625 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 4351 m= 3 mr = 63 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 0.3100000 number of dielectric boundary points 3860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2389 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9322 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2799845E-08 -1.2462066E-09 midg,1,midg; midg,igrid,midg 3.0245488E-08 -2.2478917E-08 1,midg,midg; igrid,midg,midg -1.7856992E-08 5.9381584E-08 gauss-seidel spectral radius is 0.9877242 estimated iterations to convergence 74 setup time was (sec) 0.6200000 now iterating at: 03:40:12 rms-change max change #iterations 0.1599425 21.94430 at 10iterations 1.6719492E-02 2.329584 at 20iterations 1.8183544E-03 0.2417712 at 30iterations 2.5880337E-04 3.3121109E-02 at 40iterations 6.1387778E-05 6.8225861E-03 at 50iterations finished qdiffx linear iterations at : 03:40:15 total time elapsed so far: 4.320000 # loops : 50 mean,max change (kT/e) : 6.1387778E-05 6.8225861E-03 energy calculations done at 4.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.490000 DelPhi exited at 03:40:16 4.498u 0.425s 0:05.35 91.7% 0+0k 0+0io 6pf+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 03:40:16 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 = 2765 !!! WARNING: ASP 288 has a net charge of -0.7280 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: 1.947981 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): 10.35200 65.17800 ymin,ymax (A): -5.452000 47.37900 zmin,zma (A): -6.719000 46.52800 x,y,z range (A): 54.82600 52.83100 53.24700 scale (grids/A): 1.947981 object centre (A): 37.76500 20.96350 19.90450 number of atom coordinates read : 2765 total number of charged atoms : 2617 net assigned charge : 3.772014 assigned positive charge : 420.1437 centred at (gu) : 95.84727 91.18369 91.52979 assigned negative charge : -416.3723 centred at (gu) : 95.22704 91.68497 91.67371 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83657 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23977 grid for indexing accessible points = 1.400000 m= 32206 mr = 58218 m= 5503 mr = 24160 m= 370 mr = 3543 m= 7 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 686 time to turn everything in is 0.6900000 number of dielectric boundary points 35677 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 20642 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) : 0.6493270 object centre at (A) : 37.76500 20.96350 19.90450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1098182E-02 -2.3894789E-02 midg,1,midg; midg,igrid,midg 3.1518314E-02 -7.6411138E-03 1,midg,midg; igrid,midg,midg -8.5409936E-03 8.2798041E-02 gauss-seidel spectral radius is 0.9987118 estimated iterations to convergence 221 setup time was (sec) 0.9900000 now iterating at: 03:40:18 rms-change max change #iterations 4.577206 198.3114 at 10iterations 2.200402 72.67415 at 20iterations 1.053494 32.70228 at 30iterations 0.5042846 16.11535 at 40iterations 0.2419170 8.258018 at 50iterations 0.1158863 4.191140 at 60iterations 5.5568550E-02 1.707872 at 70iterations 2.6640888E-02 0.8341532 at 80iterations 1.2871188E-02 0.4083023 at 90iterations 6.1765541E-03 0.2025528 at 100iterations 2.9794367E-03 9.6242905E-02 at 110iterations 1.4539384E-03 4.5783997E-02 at 120iterations finished qdiffx linear iterations at : 03:40:27 total time elapsed so far: 10.55000 # loops : 120 mean,max change (kT/e) : 1.4539384E-03 4.5783997E-02 energy calculations done at 10.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.71000 DelPhi exited at 03:40:28 10.719u 0.456s 0:11.75 94.9% 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 03:40:28 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 = 2765 !!! WARNING: ASP 288 has a net charge of -0.7280 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: 2.921971 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): 10.35200 65.17800 ymin,ymax (A): -5.452000 47.37900 zmin,zma (A): -6.719000 46.52800 x,y,z range (A): 54.82600 52.83100 53.24700 scale (grids/A): 2.921971 object centre (A): 37.76500 20.96350 19.90450 number of atom coordinates read : 2765 total number of charged atoms : 2617 net assigned charge : 3.772014 assigned positive charge : 420.1437 centred at (gu) : 98.77061 91.77547 92.29463 assigned negative charge : -416.3723 centred at (gu) : 97.84064 92.52724 92.51034 start vw surface at 0.1300000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 192763 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23977 grid for indexing accessible points = 1.400000 m= 101699 mr = 140377 m= 39395 mr = 83928 m= 10029 mr = 32095 m= 1610 mr = 7672 m= 115 mr = 1101 m= 0 mr = 55 time to grow re-entrant surface = 1.120000 no. cavity mid-points inaccessible to solvent = 2292 time to turn everything in is 1.840000 number of dielectric boundary points 80383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 20935 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) : 1.947981 object centre at (A) : 37.76500 20.96350 19.90450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1186516 -0.3741064 midg,1,midg; midg,igrid,midg 0.4272965 6.1900929E-02 1,midg,midg; igrid,midg,midg -6.9645576E-02 0.7832066 gauss-seidel spectral radius is 0.9992811 estimated iterations to convergence 294 setup time was (sec) 2.200000 now iterating at: 03:40:31 rms-change max change #iterations 10.62817 584.5648 at 10iterations 6.264188 148.9546 at 20iterations 3.669139 76.24042 at 30iterations 2.150846 38.73648 at 40iterations 1.255572 22.74462 at 50iterations 0.7325148 12.56313 at 60iterations 0.4267180 7.821726 at 70iterations 0.2482486 4.420105 at 80iterations 0.1444637 2.499813 at 90iterations 8.4105089E-02 1.421795 at 100iterations 4.8817307E-02 0.9169731 at 110iterations 2.8430559E-02 0.4854062 at 120iterations 1.6567320E-02 0.3277268 at 130iterations 9.6655292E-03 0.1764717 at 140iterations 5.6612566E-03 0.1252763 at 150iterations 3.3472972E-03 5.7216644E-02 at 160iterations 2.0070041E-03 3.5999298E-02 at 170iterations 1.2337553E-03 2.1003723E-02 at 180iterations finished qdiffx linear iterations at : 03:40:47 total time elapsed so far: 18.64000 # loops : 180 mean,max change (kT/e) : 1.2337553E-03 2.1003723E-02 energy calculations done at 18.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.81000 DelPhi exited at 03:40:49 18.812u 0.463s 0:20.70 93.0% 0+0k 0+0io 0pf+0w