Sun Oct 9 07:41:21 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 07:41:21 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 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: 0.7384513 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): 3.976000 48.90800 ymin,ymax (A): 21.61800 69.82700 zmin,zma (A): -7.694000 35.65800 x,y,z range (A): 44.93200 48.20900 43.35200 scale (grids/A): 0.7384513 object centre (A): 26.44200 45.72250 13.98200 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 241.2202 centred at (gu) : 90.63182 88.94264 89.32410 assigned negative charge : -250.7201 centred at (gu) : 90.67326 88.68478 89.69444 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6093 nv = 96 ne = 84 npr = 34881 no. pairs analyzed = 34881 no. exposed pairs = 2118 no. arc points = 15019 no. surface atoms = 718 nbur = 931 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 424 mr = 3310 m= 1 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.2500000 number of dielectric boundary points 3125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1232 ## 80 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6409 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3215913E-07 -4.0146776E-07 midg,1,midg; midg,igrid,midg -4.4404510E-07 2.5577998E-08 1,midg,midg; igrid,midg,midg -1.1499405E-07 -2.1594400E-07 gauss-seidel spectral radius is 0.9903974 estimated iterations to convergence 83 setup time was (sec) 0.5200000 now iterating at: 07:41:22 rms-change max change #iterations 0.2085053 39.17723 at 10iterations 2.7818475E-02 4.208149 at 20iterations 3.7097854E-03 0.5038147 at 30iterations 4.9183628E-04 7.7690125E-02 at 40iterations 6.6528402E-05 8.9950562E-03 at 50iterations finished qdiffx linear iterations at : 07:41:25 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 6.6528402E-05 8.9950562E-03 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.960000 DelPhi exited at 07:41:26 3.967u 0.258s 0:04.50 93.5% 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 07:41:26 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 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: 2.215354 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): 3.976000 48.90800 ymin,ymax (A): 21.61800 69.82700 zmin,zma (A): -7.694000 35.65800 x,y,z range (A): 44.93200 48.20900 43.35200 scale (grids/A): 2.215354 object centre (A): 26.44200 45.72250 13.98200 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 241.2202 centred at (gu) : 91.89565 86.82798 87.97251 assigned negative charge : -250.7201 centred at (gu) : 92.01988 86.05452 89.08344 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 63220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15019 grid for indexing accessible points = 1.400000 m= 26010 mr = 42494 m= 5888 mr = 19896 m= 602 mr = 4311 m= 11 mr = 314 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1251 time to turn everything in is 0.6200000 number of dielectric boundary points 28716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 12037 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) : 0.7384513 object centre at (A) : 26.44200 45.72250 13.98200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3422112E-02 -9.0058967E-02 midg,1,midg; midg,igrid,midg -9.4217181E-02 4.2330652E-02 1,midg,midg; igrid,midg,midg -5.8980234E-02 -7.1392313E-02 gauss-seidel spectral radius is 0.9988798 estimated iterations to convergence 236 setup time was (sec) 0.9000000 now iterating at: 07:41:27 rms-change max change #iterations 4.417612 182.1347 at 10iterations 2.212932 81.44218 at 20iterations 1.113134 34.60748 at 30iterations 0.5580126 19.35505 at 40iterations 0.2795168 9.355414 at 50iterations 0.1407500 4.663246 at 60iterations 7.0581011E-02 2.438622 at 70iterations 3.5579313E-02 1.126984 at 80iterations 1.7845109E-02 0.5871868 at 90iterations 8.9839203E-03 0.2992096 at 100iterations 4.4972422E-03 0.1527727 at 110iterations 2.2661593E-03 6.7951202E-02 at 120iterations finished qdiffx linear iterations at : 07:41:35 total time elapsed so far: 9.080000 # loops : 120 mean,max change (kT/e) : 2.2661593E-03 6.7951202E-02 energy calculations done at 9.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.260000 DelPhi exited at 07:41:36 9.260u 0.289s 0:09.80 97.3% 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 Sun Oct 9 2011 at 07:41:36 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: 260 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 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: 3.323031 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): 3.976000 48.90800 ymin,ymax (A): 21.61800 69.82700 zmin,zma (A): -7.694000 35.65800 x,y,z range (A): 44.93200 48.20900 43.35200 scale (grids/A): 3.323031 object centre (A): 26.44200 45.72250 13.98200 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 241.2202 centred at (gu) : 92.84348 85.24208 86.95880 assigned negative charge : -250.7201 centred at (gu) : 93.02981 84.08184 88.62521 start vw surface at 0.1400000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 145274 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15019 grid for indexing accessible points = 1.400000 m= 77800 mr = 102249 m= 34901 mr = 64333 m= 11488 mr = 29510 m= 2428 mr = 9436 m= 324 mr = 1880 m= 14 mr = 210 m= 0 mr = 2 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 4521 time to turn everything in is 1.960000 number of dielectric boundary points 64609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 12096 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) : 2.215354 object centre at (A) : 26.44200 45.72250 13.98200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3934958 -0.6619855 midg,1,midg; midg,igrid,midg -0.8113873 0.5625744 1,midg,midg; igrid,midg,midg -0.4055706 -0.5354489 gauss-seidel spectral radius is 0.9993048 estimated iterations to convergence 299 setup time was (sec) 2.280000 now iterating at: 07:41:38 rms-change max change #iterations 9.639539 327.3310 at 10iterations 5.644989 116.4438 at 20iterations 3.293094 64.36473 at 30iterations 1.921497 37.77795 at 40iterations 1.121272 20.40002 at 50iterations 0.6550098 11.52325 at 60iterations 0.3820803 7.326191 at 70iterations 0.2227473 4.242677 at 80iterations 0.1300332 2.412133 at 90iterations 7.5937115E-02 1.338669 at 100iterations 4.4185542E-02 0.7861567 at 110iterations 2.5782689E-02 0.4452477 at 120iterations 1.5051059E-02 0.2644720 at 130iterations 8.7927319E-03 0.1743660 at 140iterations 5.1340237E-03 9.0717316E-02 at 150iterations 2.9908537E-03 5.2136898E-02 at 160iterations 1.7472703E-03 3.0843735E-02 at 170iterations 1.0186002E-03 1.8232346E-02 at 180iterations finished qdiffx linear iterations at : 07:41:52 total time elapsed so far: 15.64000 # loops : 180 mean,max change (kT/e) : 1.0186002E-03 1.8232346E-02 energy calculations done at 15.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.83000 DelPhi exited at 07:41:52 15.827u 0.287s 0:16.39 98.2% 0+0k 0+0io 0pf+0w