Mon Oct 10 14:05:04 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 Mon Oct 10 2011 at 14:05:05 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 0.6784441 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): -12.95000 39.52300 ymin,ymax (A): -27.38600 20.76800 zmin,zma (A): -7.471000 37.43600 x,y,z range (A): 52.47300 48.15400 44.90700 scale (grids/A): 0.6784441 object centre (A): 13.28650 -3.309000 14.98250 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -8.099972 assigned positive charge : 322.4318 centred at (gu) : 88.84197 91.24210 88.54970 assigned negative charge : -330.5320 centred at (gu) : 89.09314 91.31021 88.65024 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6642 nv = 96 ne = 84 npr = 43852 no. pairs analyzed = 43852 no. exposed pairs = 2726 no. arc points = 19066 no. surface atoms = 913 nbur = 1223 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 410 mr = 3635 m= 4 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.3100000 number of dielectric boundary points 3344 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1728 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7537 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.7877058E-09 -4.5873751E-08 midg,1,midg; midg,igrid,midg -1.2977301E-08 -6.7361576E-08 1,midg,midg; igrid,midg,midg 3.9768210E-08 -8.1292988E-08 gauss-seidel spectral radius is 0.9886945 estimated iterations to convergence 77 setup time was (sec) 0.5700000 now iterating at: 14:05:05 rms-change max change #iterations 0.1737033 31.97785 at 10iterations 1.9427177E-02 3.032927 at 20iterations 2.1860816E-03 0.2890663 at 30iterations 2.4834971E-04 3.3407211E-02 at 40iterations 2.7719087E-05 3.9100647E-03 at 50iterations finished qdiffx linear iterations at : 14:05:09 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 2.7719087E-05 3.9100647E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 14:05:09 4.037u 0.273s 0:04.82 89.2% 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 Mon Oct 10 2011 at 14:05:09 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 2.035332 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): -12.95000 39.52300 ymin,ymax (A): -27.38600 20.76800 zmin,zma (A): -7.471000 37.43600 x,y,z range (A): 52.47300 48.15400 44.90700 scale (grids/A): 2.035332 object centre (A): 13.28650 -3.309000 14.98250 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -8.099972 assigned positive charge : 322.4318 centred at (gu) : 86.52610 93.72601 85.64887 assigned negative charge : -330.5320 centred at (gu) : 87.27945 93.93059 85.95079 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 70666 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19066 grid for indexing accessible points = 1.400000 m= 26963 mr = 48596 m= 5131 mr = 20178 m= 413 mr = 3359 m= 7 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 30881 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15802 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) : 0.6784441 object centre at (A) : 13.28650 -3.309000 14.98250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.1378873E-03 -2.9269464E-02 midg,1,midg; midg,igrid,midg 1.4473222E-03 -2.1036176E-02 1,midg,midg; igrid,midg,midg 3.5212751E-02 -8.7552056E-02 gauss-seidel spectral radius is 0.9987485 estimated iterations to convergence 224 setup time was (sec) 0.9600000 now iterating at: 14:05:11 rms-change max change #iterations 4.417714 176.4556 at 10iterations 2.141145 79.63510 at 20iterations 1.034825 31.76143 at 30iterations 0.5000903 17.77956 at 40iterations 0.2423519 8.001232 at 50iterations 0.1172348 3.851411 at 60iterations 5.6816194E-02 1.762753 at 70iterations 2.7528534E-02 1.086517 at 80iterations 1.3334163E-02 0.4258214 at 90iterations 6.4180219E-03 0.1900101 at 100iterations 3.1182552E-03 9.8573685E-02 at 110iterations 1.5051049E-03 4.8332214E-02 at 120iterations finished qdiffx linear iterations at : 14:05:19 total time elapsed so far: 9.250000 # loops : 120 mean,max change (kT/e) : 1.5051049E-03 4.8332214E-02 energy calculations done at 9.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.420000 DelPhi exited at 14:05:20 9.422u 0.272s 0:10.40 93.1% 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 Mon Oct 10 2011 at 14:05:20 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 3.052999 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): -12.95000 39.52300 ymin,ymax (A): -27.38600 20.76800 zmin,zma (A): -7.471000 37.43600 x,y,z range (A): 52.47300 48.15400 44.90700 scale (grids/A): 3.052999 object centre (A): 13.28650 -3.309000 14.98250 number of atom coordinates read : 2136 total number of charged atoms : 1995 net assigned charge : -8.099972 assigned positive charge : 322.4318 centred at (gu) : 84.78922 95.58909 83.47328 assigned negative charge : -330.5320 centred at (gu) : 85.91919 95.89582 83.92610 start vw surface at 0.1300000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 163033 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19066 grid for indexing accessible points = 1.400000 m= 84720 mr = 117453 m= 33566 mr = 69737 m= 9625 mr = 27289 m= 1830 mr = 7412 m= 136 mr = 1313 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.680000 number of dielectric boundary points 69629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 15960 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) : 2.035332 object centre at (A) : 13.28650 -3.309000 14.98250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.9339587E-02 -0.2928416 midg,1,midg; midg,igrid,midg -1.0956798E-02 -9.3869954E-02 1,midg,midg; igrid,midg,midg 0.5000107 -0.7937344 gauss-seidel spectral radius is 0.9992793 estimated iterations to convergence 294 setup time was (sec) 2.020000 now iterating at: 14:05:22 rms-change max change #iterations 10.07451 426.4160 at 10iterations 5.859504 128.9869 at 20iterations 3.402695 69.06621 at 30iterations 1.980131 38.44727 at 40iterations 1.148086 20.71601 at 50iterations 0.6640938 12.30540 at 60iterations 0.3849781 6.909958 at 70iterations 0.2222190 4.306833 at 80iterations 0.1288368 2.428974 at 90iterations 7.4649364E-02 1.321449 at 100iterations 4.3107644E-02 0.8516030 at 110iterations 2.4945224E-02 0.4412441 at 120iterations 1.4423070E-02 0.2514143 at 130iterations 8.3347484E-03 0.1449206 at 140iterations 4.8182649E-03 9.7096920E-02 at 150iterations 2.7948113E-03 4.6607971E-02 at 160iterations 1.6180481E-03 3.1314850E-02 at 170iterations 9.3866233E-04 1.7662048E-02 at 180iterations finished qdiffx linear iterations at : 14:05:36 total time elapsed so far: 15.72000 # loops : 180 mean,max change (kT/e) : 9.3866233E-04 1.7662048E-02 energy calculations done at 15.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.90000 DelPhi exited at 14:05:37 15.902u 0.347s 0:16.59 97.8% 0+0k 0+0io 0pf+0w