Tue Oct 11 07:36:48 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 07:36:48 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 = 2483 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: 0.5904989 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): -6.614000 53.67400 ymin,ymax (A): -22.51200 22.45000 zmin,zma (A): 9.023000 55.03000 x,y,z range (A): 60.28800 44.96200 46.00700 scale (grids/A): 0.5904989 object centre (A): 23.53000 -3.1001091E-02 32.02650 number of atom coordinates read : 2483 total number of charged atoms : 2346 net assigned charge : 8.500010 assigned positive charge : 377.6051 centred at (gu) : 89.60097 90.16840 89.70155 assigned negative charge : -369.1056 centred at (gu) : 89.66570 90.16670 89.53371 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5612 nv = 96 ne = 84 npr = 50585 no. pairs analyzed = 50585 no. exposed pairs = 2900 no. arc points = 20558 no. surface atoms = 988 nbur = 1495 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 267 mr = 3067 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2254 ## 327 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7226 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8717681E-09 6.4512622E-09 midg,1,midg; midg,igrid,midg 2.5313125E-09 2.8196785E-09 1,midg,midg; igrid,midg,midg 4.7376685E-09 9.1547392E-10 gauss-seidel spectral radius is 0.9851483 estimated iterations to convergence 67 setup time was (sec) 0.3800000 now iterating at: 07:36:49 rms-change max change #iterations 9.8375537E-02 18.77382 at 10iterations 8.3628399E-03 1.366520 at 20iterations 7.5032481E-04 0.1189575 at 30iterations 8.1819213E-05 1.3710022E-02 at 40iterations 1.1255762E-05 2.0446777E-03 at 50iterations finished qdiffx linear iterations at : 07:36:52 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1255762E-05 2.0446777E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 07:36:52 3.352u 0.160s 0:03.83 91.6% 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 07:36:52 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 = 2483 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: 1.771497 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): -6.614000 53.67400 ymin,ymax (A): -22.51200 22.45000 zmin,zma (A): 9.023000 55.03000 x,y,z range (A): 60.28800 44.96200 46.00700 scale (grids/A): 1.771497 object centre (A): 23.53000 -3.1001091E-02 32.02650 number of atom coordinates read : 2483 total number of charged atoms : 2346 net assigned charge : 8.500010 assigned positive charge : 377.6051 centred at (gu) : 88.80249 90.50481 89.10406 assigned negative charge : -369.1056 centred at (gu) : 88.99693 90.49985 88.60104 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 61519 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20558 grid for indexing accessible points = 1.400000 m= 20886 mr = 42692 m= 2629 mr = 15202 m= 106 mr = 1468 m= 4 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 971 time to turn everything in is 0.3000000 number of dielectric boundary points 25762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 256 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 18222 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) : 0.5904989 object centre at (A) : 23.53000 -3.1001091E-02 32.02650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1232853E-03 2.9201949E-02 midg,1,midg; midg,igrid,midg 2.4942921E-03 6.2100980E-03 1,midg,midg; igrid,midg,midg 1.3057943E-02 2.7160024E-02 gauss-seidel spectral radius is 0.9984090 estimated iterations to convergence 199 setup time was (sec) 0.5200000 now iterating at: 07:36:53 rms-change max change #iterations 3.528647 181.6016 at 10iterations 1.557088 64.23853 at 20iterations 0.6841965 26.44866 at 30iterations 0.3027473 11.35754 at 40iterations 0.1345381 4.958690 at 50iterations 5.9148800E-02 2.162680 at 60iterations 2.6083883E-02 0.9551392 at 70iterations 1.1552306E-02 0.3936691 at 80iterations 5.0998852E-03 0.1753998 at 90iterations 2.2648757E-03 7.9389572E-02 at 100iterations 1.0045832E-03 3.6003113E-02 at 110iterations 4.4614784E-04 1.6537666E-02 at 120iterations finished qdiffx linear iterations at : 07:37:00 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 4.4614784E-04 1.6537666E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 07:37:00 7.520u 0.191s 0:08.07 95.5% 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 07:37:00 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 = 2483 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: 2.657245 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): -6.614000 53.67400 ymin,ymax (A): -22.51200 22.45000 zmin,zma (A): 9.023000 55.03000 x,y,z range (A): 60.28800 44.96200 46.00700 scale (grids/A): 2.657245 object centre (A): 23.53000 -3.1001091E-02 32.02650 number of atom coordinates read : 2483 total number of charged atoms : 2346 net assigned charge : 8.500010 assigned positive charge : 377.6051 centred at (gu) : 88.20365 90.75710 88.65614 assigned negative charge : -369.1056 centred at (gu) : 88.49527 90.74965 87.90155 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 142450 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20558 grid for indexing accessible points = 1.400000 m= 69870 mr = 103553 m= 22862 mr = 57151 m= 4330 mr = 17935 m= 443 mr = 2973 m= 19 mr = 287 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 3490 time to turn everything in is 0.7600000 number of dielectric boundary points 58075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 18755 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) : 1.771497 object centre at (A) : 23.53000 -3.1001091E-02 32.02650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1607966 0.3606791 midg,1,midg; midg,igrid,midg 1.8143201E-02 2.4062650E-02 1,midg,midg; igrid,midg,midg -0.2076596 0.2411816 gauss-seidel spectral radius is 0.9991870 estimated iterations to convergence 277 setup time was (sec) 0.9800000 now iterating at: 07:37:01 rms-change max change #iterations 8.572687 335.8384 at 10iterations 4.873976 192.5837 at 20iterations 2.740567 86.46964 at 30iterations 1.537165 31.14609 at 40iterations 0.8633034 19.65728 at 50iterations 0.4839455 11.25192 at 60iterations 0.2715661 5.455925 at 70iterations 0.1516840 3.176937 at 80iterations 8.5096143E-02 1.992001 at 90iterations 4.7518343E-02 0.9983234 at 100iterations 2.6542777E-02 0.5899944 at 110iterations 1.4884163E-02 0.3528976 at 120iterations 8.3343973E-03 0.1824799 at 130iterations 4.6694386E-03 0.1020508 at 140iterations 2.6089144E-03 5.2960515E-02 at 150iterations 1.4675474E-03 3.1676292E-02 at 160iterations 8.2484988E-04 1.6141891E-02 at 170iterations 4.6549740E-04 9.4032288E-03 at 180iterations finished qdiffx linear iterations at : 07:37:12 total time elapsed so far: 11.81000 # loops : 180 mean,max change (kT/e) : 4.6549740E-04 9.4032288E-03 energy calculations done at 11.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.95000 DelPhi exited at 07:37:13 11.951u 0.200s 0:12.45 97.5% 0+0k 0+0io 0pf+0w