Sun Oct 9 13:07:19 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 Sun Oct 9 2011 at 13:07:19 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 = 2567 !!! WARNING: HIR 42 has a net charge of 0.5140 !!! WARNING: GLM 182 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: 0.7355676 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): 0.6899999 48.92900 ymin,ymax (A): -27.05000 21.34800 zmin,zma (A): 39.55900 87.35300 x,y,z range (A): 48.23900 48.39800 47.79400 scale (grids/A): 0.7355676 object centre (A): 24.80950 -2.851001 63.45600 number of atom coordinates read : 2567 total number of charged atoms : 2448 net assigned charge : -0.5799704 assigned positive charge : 399.5618 centred at (gu) : 89.41899 89.61368 91.34989 assigned negative charge : -400.1423 centred at (gu) : 89.27978 89.62030 91.30748 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 9572 nv = 96 ne = 84 npr = 51438 no. pairs analyzed = 51438 no. exposed pairs = 3215 no. arc points = 22003 no. surface atoms = 1080 nbur = 1487 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 692 mr = 5548 m= 4 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1905 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 10394 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.5020254E-08 5.2249099E-08 midg,1,midg; midg,igrid,midg -1.2467638E-09 -1.5382769E-08 1,midg,midg; igrid,midg,midg -1.9262882E-07 1.3420406E-07 gauss-seidel spectral radius is 0.9904110 estimated iterations to convergence 83 setup time was (sec) 0.3900000 now iterating at: 13:07:20 rms-change max change #iterations 0.2711885 34.13162 at 10iterations 3.6608953E-02 4.489201 at 20iterations 5.0128838E-03 0.6404428 at 30iterations 7.6187024E-04 8.5203171E-02 at 40iterations 1.5501629E-04 1.7225266E-02 at 50iterations finished qdiffx linear iterations at : 13:07:23 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.5501629E-04 1.7225266E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 13:07:23 3.419u 0.173s 0:03.87 92.5% 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 Sun Oct 9 2011 at 13:07:23 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 = 2567 !!! WARNING: HIR 42 has a net charge of 0.5140 !!! WARNING: GLM 182 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: 2.206703 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): 0.6899999 48.92900 ymin,ymax (A): -27.05000 21.34800 zmin,zma (A): 39.55900 87.35300 x,y,z range (A): 48.23900 48.39800 47.79400 scale (grids/A): 2.206703 object centre (A): 24.80950 -2.851001 63.45600 number of atom coordinates read : 2567 total number of charged atoms : 2448 net assigned charge : -0.5799704 assigned positive charge : 399.5618 centred at (gu) : 88.25620 88.84046 94.04931 assigned negative charge : -400.1423 centred at (gu) : 87.83888 88.86066 93.92197 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 100900 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22003 grid for indexing accessible points = 1.400000 m= 41815 mr = 71598 m= 8615 mr = 32235 m= 827 mr = 5829 m= 22 mr = 425 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 42092 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 19504 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) : 0.7355676 object centre at (A) : 24.80950 -2.851001 63.45600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6139772E-02 1.4424678E-02 midg,1,midg; midg,igrid,midg -7.2853118E-02 -4.7955692E-02 1,midg,midg; igrid,midg,midg -6.0114201E-02 1.2511688E-02 gauss-seidel spectral radius is 0.9989551 estimated iterations to convergence 245 setup time was (sec) 0.7200000 now iterating at: 13:07:24 rms-change max change #iterations 5.776711 219.2227 at 10iterations 2.961051 84.80007 at 20iterations 1.528812 44.20361 at 30iterations 0.7870370 19.69861 at 40iterations 0.4056418 11.04352 at 50iterations 0.2090527 6.257977 at 60iterations 0.1078611 3.032860 at 70iterations 5.5657431E-02 1.349092 at 80iterations 2.8733730E-02 0.7168751 at 90iterations 1.4822206E-02 0.4172673 at 100iterations 7.6644355E-03 0.2091084 at 110iterations 3.9774175E-03 0.1043091 at 120iterations finished qdiffx linear iterations at : 13:07:31 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 3.9774175E-03 0.1043091 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.110000 DelPhi exited at 13:07:32 8.112u 0.209s 0:08.59 96.7% 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 Sun Oct 9 2011 at 13:07:32 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 = 2567 !!! WARNING: HIR 42 has a net charge of 0.5140 !!! WARNING: GLM 182 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: 3.310054 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): 0.6899999 48.92900 ymin,ymax (A): -27.05000 21.34800 zmin,zma (A): 39.55900 87.35300 x,y,z range (A): 48.23900 48.39800 47.79400 scale (grids/A): 3.310054 object centre (A): 24.80950 -2.851001 63.45600 number of atom coordinates read : 2567 total number of charged atoms : 2448 net assigned charge : -0.5799704 assigned positive charge : 399.5618 centred at (gu) : 87.38410 88.26057 96.07381 assigned negative charge : -400.1423 centred at (gu) : 86.75827 88.29092 95.88283 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 232366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22003 grid for indexing accessible points = 1.400000 m= 128509 mr = 172243 m= 54483 mr = 107388 m= 16343 mr = 45454 m= 3328 mr = 12825 m= 407 mr = 2412 m= 24 mr = 239 m= 0 mr = 6 time to grow re-entrant surface = 0.8399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.580000 number of dielectric boundary points 94893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 19584 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) : 2.206703 object centre at (A) : 24.80950 -2.851001 63.45600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3613135 -0.1785201 midg,1,midg; midg,igrid,midg -1.450495 -0.7607560 1,midg,midg; igrid,midg,midg -0.7179698 6.2787333E-03 gauss-seidel spectral radius is 0.9993340 estimated iterations to convergence 306 setup time was (sec) 1.840000 now iterating at: 13:07:34 rms-change max change #iterations 12.55977 401.1003 at 10iterations 7.564662 147.1393 at 20iterations 4.540369 86.47221 at 30iterations 2.723219 44.27453 at 40iterations 1.627853 24.75252 at 50iterations 0.9714377 15.59862 at 60iterations 0.5784757 9.340052 at 70iterations 0.3449937 5.391636 at 80iterations 0.2051731 3.081775 at 90iterations 0.1217759 1.823495 at 100iterations 7.2531097E-02 1.077881 at 110iterations 4.2966433E-02 0.6546745 at 120iterations 2.5673714E-02 0.3751059 at 130iterations 1.5294136E-02 0.2268915 at 140iterations 9.1592437E-03 0.1530724 at 150iterations 5.5397418E-03 8.2523346E-02 at 160iterations 3.4025172E-03 5.7239532E-02 at 170iterations 2.1291226E-03 4.2769432E-02 at 180iterations finished qdiffx linear iterations at : 13:07:46 total time elapsed so far: 13.68000 # loops : 180 mean,max change (kT/e) : 2.1291226E-03 4.2769432E-02 energy calculations done at 13.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.82000 DelPhi exited at 13:07:46 13.817u 0.210s 0:14.39 97.4% 0+0k 0+0io 0pf+0w