Mon Oct 10 17:05:31 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 17:05:31 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2763 !!! WARNING: HIT 107 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6231184 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): 14.38100 71.51300 ymin,ymax (A): 35.36000 82.28100 zmin,zma (A): 61.92900 117.2040 x,y,z range (A): 57.13200 46.92100 55.27500 scale (grids/A): 0.6231184 object centre (A): 42.94700 58.82050 89.56650 number of atom coordinates read : 2763 total number of charged atoms : 2622 net assigned charge : -6.485979 assigned positive charge : 414.3643 centred at (gu) : 88.83591 89.45512 88.80470 assigned negative charge : -420.8513 centred at (gu) : 88.79522 89.34458 88.75956 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7258 nv = 96 ne = 84 npr = 55480 no. pairs analyzed = 55480 no. exposed pairs = 3606 no. arc points = 25638 no. surface atoms = 1212 nbur = 1551 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 337 mr = 3801 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.3100000 number of dielectric boundary points 3764 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2580 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8933 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1858613E-08 -1.6289993E-09 midg,1,midg; midg,igrid,midg -1.6198829E-08 2.6322780E-09 1,midg,midg; igrid,midg,midg -1.1318762E-08 -1.9061179E-09 gauss-seidel spectral radius is 0.9866844 estimated iterations to convergence 71 setup time was (sec) 0.5900000 now iterating at: 17:05:32 rms-change max change #iterations 0.1333739 19.12914 at 10iterations 1.2474354E-02 1.744215 at 20iterations 1.1754355E-03 0.1964989 at 30iterations 1.0978074E-04 1.5963554E-02 at 40iterations 1.0411109E-05 1.3437271E-03 at 50iterations finished qdiffx linear iterations at : 17:05:35 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 1.0411109E-05 1.3437271E-03 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 17:05:36 4.372u 0.305s 0:05.17 90.3% 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 17:05:36 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2763 !!! WARNING: HIT 107 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.869355 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): 14.38100 71.51300 ymin,ymax (A): 35.36000 82.28100 zmin,zma (A): 61.92900 117.2040 x,y,z range (A): 57.13200 46.92100 55.27500 scale (grids/A): 1.869355 object centre (A): 42.94700 58.82050 89.56650 number of atom coordinates read : 2763 total number of charged atoms : 2622 net assigned charge : -6.485979 assigned positive charge : 414.3643 centred at (gu) : 86.50665 88.36482 86.41331 assigned negative charge : -420.8513 centred at (gu) : 86.38538 88.03347 86.27847 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 79297 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25638 grid for indexing accessible points = 1.400000 m= 26294 mr = 53843 m= 3479 mr = 18526 m= 153 mr = 1981 m= 0 mr = 36 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 900 time to turn everything in is 0.6000000 number of dielectric boundary points 34837 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 202 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20561 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) : 0.6231184 object centre at (A) : 42.94700 58.82050 89.56650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3078025E-03 -5.1497743E-03 midg,1,midg; midg,igrid,midg -3.1840269E-02 -1.8039981E-03 1,midg,midg; igrid,midg,midg -6.0892180E-02 2.0551290E-03 gauss-seidel spectral radius is 0.9986073 estimated iterations to convergence 212 setup time was (sec) 0.9400000 now iterating at: 17:05:37 rms-change max change #iterations 4.271771 175.8376 at 10iterations 1.976084 65.48946 at 20iterations 0.9163556 28.44962 at 30iterations 0.4244818 13.01738 at 40iterations 0.1975078 5.935336 at 50iterations 9.1857128E-02 3.151705 at 60iterations 4.2640984E-02 1.480714 at 70iterations 1.9747060E-02 0.5888529 at 80iterations 9.1691865E-03 0.3088188 at 90iterations 4.2687347E-03 0.1368045 at 100iterations 1.9846277E-03 6.3838959E-02 at 110iterations 9.2282507E-04 3.1909943E-02 at 120iterations finished qdiffx linear iterations at : 17:05:46 total time elapsed so far: 9.890000 # loops : 120 mean,max change (kT/e) : 9.2282507E-04 3.1909943E-02 energy calculations done at 9.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.07000 DelPhi exited at 17:05:47 10.073u 0.326s 0:10.79 96.2% 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 17:05:47 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2763 !!! WARNING: HIT 107 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.804033 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): 14.38100 71.51300 ymin,ymax (A): 35.36000 82.28100 zmin,zma (A): 61.92900 117.2040 x,y,z range (A): 57.13200 46.92100 55.27500 scale (grids/A): 2.804033 object centre (A): 42.94700 58.82050 89.56650 number of atom coordinates read : 2763 total number of charged atoms : 2622 net assigned charge : -6.485979 assigned positive charge : 414.3643 centred at (gu) : 84.75991 87.54710 84.61978 assigned negative charge : -420.8513 centred at (gu) : 84.57807 87.05009 84.41759 start vw surface at 0.1400000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 183418 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25638 grid for indexing accessible points = 1.400000 m= 87720 mr = 130917 m= 28993 mr = 70179 m= 6005 mr = 22468 m= 669 mr = 4239 m= 27 mr = 404 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 2917 time to turn everything in is 1.510000 number of dielectric boundary points 78620 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 20973 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) : 1.869355 object centre at (A) : 42.94700 58.82050 89.56650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2154963 -0.3033907 midg,1,midg; midg,igrid,midg -0.3375707 -5.8863584E-02 1,midg,midg; igrid,midg,midg -0.6833143 0.1461757 gauss-seidel spectral radius is 0.9992716 estimated iterations to convergence 292 setup time was (sec) 1.900000 now iterating at: 17:05:49 rms-change max change #iterations 10.34020 423.0137 at 10iterations 6.154628 152.3608 at 20iterations 3.615043 82.46920 at 30iterations 2.119391 47.36488 at 40iterations 1.236254 28.53216 at 50iterations 0.7189721 13.89692 at 60iterations 0.4172064 9.017362 at 70iterations 0.2418668 4.686951 at 80iterations 0.1401357 2.813782 at 90iterations 8.1016459E-02 1.554603 at 100iterations 4.6881407E-02 0.9452133 at 110iterations 2.7112961E-02 0.5138626 at 120iterations 1.5657298E-02 0.3096657 at 130iterations 9.0480922E-03 0.1629410 at 140iterations 5.2231373E-03 0.1029854 at 150iterations 3.0187527E-03 5.4293633E-02 at 160iterations 1.7433641E-03 3.2101750E-02 at 170iterations 1.0076534E-03 1.7690420E-02 at 180iterations finished qdiffx linear iterations at : 17:06:03 total time elapsed so far: 16.35000 # loops : 180 mean,max change (kT/e) : 1.0076534E-03 1.7690420E-02 energy calculations done at 16.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.54000 DelPhi exited at 17:06:04 16.538u 0.351s 0:17.33 97.4% 0+0k 0+0io 0pf+0w