Mon Oct 10 14:01:18 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 14:01:18 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5414 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5314305 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): 15.53000 80.58000 ymin,ymax (A): 18.07100 84.72500 zmin,zma (A): 1.415000 68.40400 x,y,z range (A): 65.05000 66.65400 66.98900 scale (grids/A): 0.5314305 object centre (A): 48.05500 51.39800 34.90950 number of atom coordinates read : 5414 total number of charged atoms : 5249 net assigned charge : -1.485992 assigned positive charge : 814.5073 centred at (gu) : 90.52273 89.15090 90.53719 assigned negative charge : -815.9997 centred at (gu) : 90.42110 89.21883 90.64702 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 9856 nv = 96 ne = 84 npr = 108533 no. pairs analyzed = 108533 no. exposed pairs = 6929 no. arc points = 47807 no. surface atoms = 2318 nbur = 3096 mkacc time = 0.2400000 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 = 1.624000 m= 342 mr = 5076 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.5200000 number of dielectric boundary points 5106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4821 ## 655 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 13100 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0945887E-10 -9.5498476E-10 midg,1,midg; midg,igrid,midg 5.1740284E-10 -4.2846821E-10 1,midg,midg; igrid,midg,midg -6.7544087E-10 7.3807171E-10 gauss-seidel spectral radius is 0.9819385 estimated iterations to convergence 61 setup time was (sec) 0.7700000 now iterating at: 14:01:19 rms-change max change #iterations 8.8931732E-02 12.97017 at 10iterations 5.9376671E-03 0.7836113 at 20iterations 7.1667787E-04 0.1423149 at 30iterations 1.9898541E-04 4.2972565E-02 at 40iterations 6.5005690E-05 1.3496399E-02 at 50iterations finished qdiffx linear iterations at : 14:01:21 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 6.5005690E-05 1.3496399E-02 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 14:01:22 3.693u 0.251s 0:05.23 75.3% 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 Mon Oct 10 2011 at 14:01:23 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5414 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.594292 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): 15.53000 80.58000 ymin,ymax (A): 18.07100 84.72500 zmin,zma (A): 1.415000 68.40400 x,y,z range (A): 65.05000 66.65400 66.98900 scale (grids/A): 1.594292 object centre (A): 48.05500 51.39800 34.90950 number of atom coordinates read : 5414 total number of charged atoms : 5249 net assigned charge : -1.485992 assigned positive charge : 814.5073 centred at (gu) : 91.56680 87.45097 91.61017 assigned negative charge : -815.9997 centred at (gu) : 91.26313 87.65643 91.94053 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 110181 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47807 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 33390 mr = 75564 m= 3135 mr = 22332 m= 78 mr = 1414 m= 0 mr = 7 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 462 time to turn everything in is 0.7600000 number of dielectric boundary points 47467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 614 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 39901 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) : 0.5314305 object centre at (A) : 48.05500 51.39800 34.90950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3143358E-02 -5.1014192E-02 midg,1,midg; midg,igrid,midg -4.5662131E-03 -2.2928992E-02 1,midg,midg; igrid,midg,midg -2.0460687E-03 2.0953774E-02 gauss-seidel spectral radius is 0.9983402 estimated iterations to convergence 195 setup time was (sec) 1.090000 now iterating at: 14:01:24 rms-change max change #iterations 4.491885 165.8740 at 10iterations 1.941879 60.32069 at 20iterations 0.8408602 24.16666 at 30iterations 0.3636151 10.60735 at 40iterations 0.1578302 4.380310 at 50iterations 6.8570562E-02 2.019053 at 60iterations 2.9801726E-02 0.8790436 at 70iterations 1.2974980E-02 0.3767891 at 80iterations 5.6736358E-03 0.1679182 at 90iterations 2.4950923E-03 7.3059082E-02 at 100iterations 1.1171643E-03 3.2669067E-02 at 110iterations 5.1704026E-04 1.6105652E-02 at 120iterations finished qdiffx linear iterations at : 14:01:33 total time elapsed so far: 9.410000 # loops : 120 mean,max change (kT/e) : 5.1704026E-04 1.6105652E-02 energy calculations done at 9.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.620000 DelPhi exited at 14:01:33 9.625u 0.220s 0:10.42 94.4% 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 14:01:33 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5414 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.391438 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): 15.53000 80.58000 ymin,ymax (A): 18.07100 84.72500 zmin,zma (A): 1.415000 68.40400 x,y,z range (A): 65.05000 66.65400 66.98900 scale (grids/A): 2.391438 object centre (A): 48.05500 51.39800 34.90950 number of atom coordinates read : 5414 total number of charged atoms : 5249 net assigned charge : -1.485992 assigned positive charge : 814.5073 centred at (gu) : 92.34945 86.17619 92.41486 assigned negative charge : -815.9997 centred at (gu) : 91.89474 86.48460 92.91066 start vw surface at 0.2200000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 256481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47807 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 117710 mr = 185703 m= 31554 mr = 91956 m= 4736 mr = 23018 m= 302 mr = 2979 m= 4 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 1549 time to turn everything in is 1.910000 number of dielectric boundary points 107015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 51 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 41920 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) : 1.594292 object centre at (A) : 48.05500 51.39800 34.90950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1723824 -1.082340 midg,1,midg; midg,igrid,midg -0.2928609 -0.3848479 1,midg,midg; igrid,midg,midg 0.1581886 0.4815304 gauss-seidel spectral radius is 0.9992514 estimated iterations to convergence 288 setup time was (sec) 2.250000 now iterating at: 14:01:36 rms-change max change #iterations 11.86560 307.0926 at 10iterations 7.078764 163.0858 at 20iterations 4.182067 79.33762 at 30iterations 2.464225 49.93864 at 40iterations 1.440055 33.10896 at 50iterations 0.8404294 19.23961 at 60iterations 0.4881612 8.908905 at 70iterations 0.2831024 5.010033 at 80iterations 0.1641866 2.925304 at 90iterations 9.4886743E-02 1.884791 at 100iterations 5.4802801E-02 0.9705463 at 110iterations 3.1644933E-02 0.5328074 at 120iterations 1.8264698E-02 0.3308754 at 130iterations 1.0541162E-02 0.1782818 at 140iterations 6.0643465E-03 0.1015418 at 150iterations 3.5082637E-03 5.7271004E-02 at 160iterations 2.0248983E-03 3.3560753E-02 at 170iterations 1.1755262E-03 1.9552231E-02 at 180iterations finished qdiffx linear iterations at : 14:01:47 total time elapsed so far: 13.63000 # loops : 180 mean,max change (kT/e) : 1.1755262E-03 1.9552231E-02 energy calculations done at 13.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.85000 DelPhi exited at 14:01:49 13.855u 0.328s 0:15.23 93.0% 0+0k 0+0io 0pf+0w