Tue Oct 11 05:28:07 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 Tue Oct 11 2011 at 05:28:07 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2214 !!! WARNING: HIZ 40 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: ZN6 658 has a net charge of 1.4000 !!! WARNING: ZN6 659 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7048528 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): 17.34200 63.23200 ymin,ymax (A): -3.560000 33.62200 zmin,zma (A): 21.33200 71.83900 x,y,z range (A): 45.89000 37.18200 50.50700 scale (grids/A): 0.7048528 object centre (A): 40.28700 15.03100 46.58550 number of atom coordinates read : 2214 total number of charged atoms : 1949 net assigned charge : 9.525008 assigned positive charge : 317.9370 centred at (gu) : 90.90532 89.65253 88.82677 assigned negative charge : -308.4121 centred at (gu) : 91.04829 89.64100 88.79338 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6919 nv = 96 ne = 84 npr = 39451 no. pairs analyzed = 39451 no. exposed pairs = 2483 no. arc points = 16908 no. surface atoms = 854 nbur = 1360 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 3985 m= 3 mr = 90 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3318 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1631 ## 174 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7772 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5898079E-08 7.3427763E-08 midg,1,midg; midg,igrid,midg 7.5859120E-08 7.6475963E-08 1,midg,midg; igrid,midg,midg 1.1859592E-07 1.0562893E-08 gauss-seidel spectral radius is 0.9895043 estimated iterations to convergence 79 setup time was (sec) 0.5200000 now iterating at: 05:28:07 rms-change max change #iterations 0.2063741 36.13235 at 10iterations 2.5213107E-02 3.879227 at 20iterations 3.0664038E-03 0.3902760 at 30iterations 3.8124411E-04 6.8092346E-02 at 40iterations 5.3201278E-05 7.8182220E-03 at 50iterations finished qdiffx linear iterations at : 05:28:10 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 5.3201278E-05 7.8182220E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 05:28:11 3.450u 0.167s 0:03.98 90.7% 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 05:28:11 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2214 !!! WARNING: HIZ 40 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: ZN6 658 has a net charge of 1.4000 !!! WARNING: ZN6 659 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.114558 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): 17.34200 63.23200 ymin,ymax (A): -3.560000 33.62200 zmin,zma (A): 21.33200 71.83900 x,y,z range (A): 45.89000 37.18200 50.50700 scale (grids/A): 2.114558 object centre (A): 40.28700 15.03100 46.58550 number of atom coordinates read : 2214 total number of charged atoms : 1949 net assigned charge : 9.525008 assigned positive charge : 317.9370 centred at (gu) : 92.71597 88.95771 86.48029 assigned negative charge : -308.4121 centred at (gu) : 93.14503 88.92310 86.38012 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 73065 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16908 grid for indexing accessible points = 1.400000 m= 30140 mr = 51773 m= 6094 mr = 23186 m= 500 mr = 4075 m= 5 mr = 239 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 368 time to turn everything in is 0.5900000 number of dielectric boundary points 30531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 70 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15464 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) : 0.7048528 object centre at (A) : 40.28700 15.03100 46.58550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8416598E-02 5.4181587E-02 midg,1,midg; midg,igrid,midg 2.8353507E-02 2.7150782E-02 1,midg,midg; igrid,midg,midg 4.0520422E-02 3.5402603E-02 gauss-seidel spectral radius is 0.9988191 estimated iterations to convergence 230 setup time was (sec) 0.9100000 now iterating at: 05:28:12 rms-change max change #iterations 4.578323 216.7244 at 10iterations 2.259212 74.17635 at 20iterations 1.120264 40.07671 at 30iterations 0.5543928 16.11675 at 40iterations 0.2738431 9.090431 at 50iterations 0.1359248 4.473312 at 60iterations 6.7405552E-02 1.904848 at 70iterations 3.3281989E-02 0.9817238 at 80iterations 1.6456192E-02 0.5218565 at 90iterations 8.1599550E-03 0.2601309 at 100iterations 4.0602777E-03 0.1276035 at 110iterations 2.0216808E-03 5.7971954E-02 at 120iterations finished qdiffx linear iterations at : 05:28:19 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.0216808E-03 5.7971954E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 05:28:19 8.002u 0.235s 0:08.54 96.3% 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 05:28:19 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2214 !!! WARNING: HIZ 40 has a net charge of 0.2000 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: ZN6 658 has a net charge of 1.4000 !!! WARNING: ZN6 659 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.171837 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): 17.34200 63.23200 ymin,ymax (A): -3.560000 33.62200 zmin,zma (A): 21.33200 71.83900 x,y,z range (A): 45.89000 37.18200 50.50700 scale (grids/A): 3.171837 object centre (A): 40.28700 15.03100 46.58550 number of atom coordinates read : 2214 total number of charged atoms : 1949 net assigned charge : 9.525008 assigned positive charge : 317.9370 centred at (gu) : 94.07388 88.43661 84.72041 assigned negative charge : -308.4121 centred at (gu) : 94.71757 88.38465 84.57017 start vw surface at 0.1600000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 168006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16908 grid for indexing accessible points = 1.400000 m= 93020 mr = 124469 m= 39126 mr = 77674 m= 11570 mr = 32415 m= 2230 mr = 8988 m= 202 mr = 1652 m= 4 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 1151 time to turn everything in is 1.860000 number of dielectric boundary points 68854 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 15592 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) : 2.114558 object centre at (A) : 40.28700 15.03100 46.58550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4991976 0.3879274 midg,1,midg; midg,igrid,midg 0.2320514 0.2272597 1,midg,midg; igrid,midg,midg 0.3306509 0.5513762 gauss-seidel spectral radius is 0.9992946 estimated iterations to convergence 297 setup time was (sec) 2.180000 now iterating at: 05:28:22 rms-change max change #iterations 10.23298 362.3254 at 10iterations 6.060176 144.9060 at 20iterations 3.589132 77.37778 at 30iterations 2.120632 40.36458 at 40iterations 1.249885 23.78310 at 50iterations 0.7345699 15.38202 at 60iterations 0.4317287 8.419313 at 70iterations 0.2533194 4.602937 at 80iterations 0.1483555 2.666848 at 90iterations 8.6962700E-02 1.581236 at 100iterations 5.0925348E-02 0.9840202 at 110iterations 2.9805101E-02 0.5268860 at 120iterations 1.7466091E-02 0.3139930 at 130iterations 1.0282439E-02 0.1793327 at 140iterations 6.0886070E-03 0.1071072 at 150iterations 3.6477468E-03 7.0642471E-02 at 160iterations 2.2463480E-03 4.3622971E-02 at 170iterations 1.4446052E-03 2.8640747E-02 at 180iterations finished qdiffx linear iterations at : 05:28:33 total time elapsed so far: 13.09000 # loops : 180 mean,max change (kT/e) : 1.4446052E-03 2.8640747E-02 energy calculations done at 13.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.27000 DelPhi exited at 05:28:33 13.277u 0.263s 0:14.22 95.1% 0+0k 0+0io 0pf+0w