Tue Oct 11 08:10:39 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 08:10:39 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1806 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: HIZ 166 has a net charge of 0.2000 !!! WARNING: ZN4 400 has a net charge of 1.4000 !!! WARNING: ZN4 401 has a net charge of 1.4000 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: 0.7270796 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): -17.00200 31.96100 ymin,ymax (A): 18.37000 63.44100 zmin,zma (A): -22.85200 26.03800 x,y,z range (A): 48.96300 45.07100 48.89000 scale (grids/A): 0.7270796 object centre (A): 7.479500 40.90550 1.593000 number of atom coordinates read : 1806 total number of charged atoms : 1666 net assigned charge : 4.700003 assigned positive charge : 262.0494 centred at (gu) : 91.18643 91.72205 89.14909 assigned negative charge : -257.3494 centred at (gu) : 91.15041 91.83809 89.20423 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6822 nv = 96 ne = 84 npr = 34486 no. pairs analyzed = 34486 no. exposed pairs = 2724 no. arc points = 20025 no. surface atoms = 905 nbur = 901 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 3172 m= 8 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1568 ## 117 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1377949E-07 2.4607548E-08 midg,1,midg; midg,igrid,midg 9.7147222E-08 -1.5988819E-08 1,midg,midg; igrid,midg,midg 3.2790151E-08 1.0639228E-07 gauss-seidel spectral radius is 0.9901314 estimated iterations to convergence 82 setup time was (sec) 0.5000000 now iterating at: 08:10:40 rms-change max change #iterations 0.2110467 28.95225 at 10iterations 2.6538916E-02 3.565035 at 20iterations 3.4460751E-03 0.5716057 at 30iterations 4.4488534E-04 6.4287186E-02 at 40iterations 5.6403762E-05 8.0924034E-03 at 50iterations finished qdiffx linear iterations at : 08:10:44 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 5.6403762E-05 8.0924034E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 08:10:44 4.273u 0.281s 0:05.15 88.3% 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 08:10:45 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1806 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: HIZ 166 has a net charge of 0.2000 !!! WARNING: ZN4 400 has a net charge of 1.4000 !!! WARNING: ZN4 401 has a net charge of 1.4000 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: 2.181239 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): -17.00200 31.96100 ymin,ymax (A): 18.37000 63.44100 zmin,zma (A): -22.85200 26.03800 x,y,z range (A): 48.96300 45.07100 48.89000 scale (grids/A): 2.181239 object centre (A): 7.479500 40.90550 1.593000 number of atom coordinates read : 1806 total number of charged atoms : 1666 net assigned charge : 4.700003 assigned positive charge : 262.0494 centred at (gu) : 93.55948 95.16640 87.44769 assigned negative charge : -257.3494 centred at (gu) : 93.45135 95.51431 87.61279 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70846 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20025 grid for indexing accessible points = 1.400000 m= 24893 mr = 43797 m= 4558 mr = 16886 m= 364 mr = 2514 m= 7 mr = 122 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 37347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 13262 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) : 0.7270796 object centre at (A) : 7.479500 40.90550 1.593000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3937254E-02 -1.7008435E-02 midg,1,midg; midg,igrid,midg 3.3852585E-02 2.5896624E-02 1,midg,midg; igrid,midg,midg 1.0793703E-03 -5.3312480E-03 gauss-seidel spectral radius is 0.9988905 estimated iterations to convergence 238 setup time was (sec) 0.9000000 now iterating at: 08:10:46 rms-change max change #iterations 4.483905 213.6856 at 10iterations 2.258471 77.37324 at 20iterations 1.149683 39.39196 at 30iterations 0.5804576 18.76747 at 40iterations 0.2936718 9.128389 at 50iterations 0.1487765 4.542031 at 60iterations 7.5002164E-02 2.890821 at 70iterations 3.7945181E-02 1.194841 at 80iterations 1.9142978E-02 0.5683746 at 90iterations 9.6349213E-03 0.3091345 at 100iterations 4.8697870E-03 0.1564789 at 110iterations 2.4571265E-03 7.8442574E-02 at 120iterations finished qdiffx linear iterations at : 08:10:55 total time elapsed so far: 9.860000 # loops : 120 mean,max change (kT/e) : 2.4571265E-03 7.8442574E-02 energy calculations done at 9.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.04000 DelPhi exited at 08:10:55 10.045u 0.310s 0:10.68 96.9% 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 08:10:55 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1806 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: HIZ 166 has a net charge of 0.2000 !!! WARNING: ZN4 400 has a net charge of 1.4000 !!! WARNING: ZN4 401 has a net charge of 1.4000 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: 3.271858 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): -17.00200 31.96100 ymin,ymax (A): 18.37000 63.44100 zmin,zma (A): -22.85200 26.03800 x,y,z range (A): 48.96300 45.07100 48.89000 scale (grids/A): 3.271858 object centre (A): 7.479500 40.90550 1.593000 number of atom coordinates read : 1806 total number of charged atoms : 1666 net assigned charge : 4.700003 assigned positive charge : 262.0494 centred at (gu) : 95.33927 97.74973 86.17160 assigned negative charge : -257.3494 centred at (gu) : 95.17713 98.27163 86.41932 start vw surface at 0.1100000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 162893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20025 grid for indexing accessible points = 1.400000 m= 77944 mr = 107013 m= 30002 mr = 60146 m= 8109 mr = 22580 m= 1374 mr = 5572 m= 117 mr = 829 m= 5 mr = 60 m= 0 mr = 2 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.760000 number of dielectric boundary points 84242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 13328 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) : 2.181239 object centre at (A) : 7.479500 40.90550 1.593000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6170156 -0.2679032 midg,1,midg; midg,igrid,midg 0.1842112 0.2031732 1,midg,midg; igrid,midg,midg -0.1017481 4.7597069E-02 gauss-seidel spectral radius is 0.9993579 estimated iterations to convergence 311 setup time was (sec) 2.110000 now iterating at: 08:10:58 rms-change max change #iterations 10.11599 362.2753 at 10iterations 6.213314 158.1655 at 20iterations 3.773993 93.53070 at 30iterations 2.295294 55.60764 at 40iterations 1.391015 28.79102 at 50iterations 0.8391746 17.51421 at 60iterations 0.5064602 9.478659 at 70iterations 0.3038020 5.586494 at 80iterations 0.1825500 3.538151 at 90iterations 0.1097124 2.212721 at 100iterations 6.5728545E-02 1.323337 at 110iterations 3.9352015E-02 0.8290054 at 120iterations 2.3594880E-02 0.4547729 at 130iterations 1.4084613E-02 0.2825394 at 140iterations 8.4498255E-03 0.1491852 at 150iterations 5.0472468E-03 9.2574120E-02 at 160iterations 3.0196335E-03 5.6097984E-02 at 170iterations 1.8028213E-03 3.2619476E-02 at 180iterations finished qdiffx linear iterations at : 08:11:13 total time elapsed so far: 16.78000 # loops : 180 mean,max change (kT/e) : 1.8028213E-03 3.2619476E-02 energy calculations done at 16.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.96000 DelPhi exited at 08:11:14 16.964u 0.342s 0:18.28 94.6% 0+0k 0+0io 0pf+0w