Sun Oct 9 02:10:54 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 02:10:55 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1859 !!! WARNING: HIR 75 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6141955 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): 87.55900 139.6330 ymin,ymax (A): 78.79100 116.4830 zmin,zma (A): -4.488000 53.47400 x,y,z range (A): 52.07401 37.69200 57.96200 scale (grids/A): 0.6141955 object centre (A): 113.5960 97.63700 24.49300 number of atom coordinates read : 1859 total number of charged atoms : 1723 net assigned charge : 6.514015 assigned positive charge : 271.0462 centred at (gu) : 88.45956 90.31748 90.53940 assigned negative charge : -264.5324 centred at (gu) : 88.57078 90.32134 90.61224 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 4722 nv = 96 ne = 84 npr = 36387 no. pairs analyzed = 36387 no. exposed pairs = 2832 no. arc points = 20547 no. surface atoms = 935 nbur = 924 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 253 mr = 2061 m= 0 mr = 11 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1500000 number of dielectric boundary points 2903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1985 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.2100000 number of grid points assigned charge 5733 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.2889960E-09 1.6860020E-09 midg,1,midg; midg,igrid,midg 4.1733745E-09 4.4672501E-09 1,midg,midg; igrid,midg,midg 1.1985883E-08 7.4756763E-11 gauss-seidel spectral radius is 0.9862215 estimated iterations to convergence 70 setup time was (sec) 0.3500000 now iterating at: 02:10:55 rms-change max change #iterations 9.4346784E-02 17.08319 at 10iterations 8.3977254E-03 1.529205 at 20iterations 8.1212859E-04 0.1457100 at 30iterations 1.0086316E-04 1.6792297E-02 at 40iterations 1.8679240E-05 2.4871826E-03 at 50iterations finished qdiffx linear iterations at : 02:10:58 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 1.8679240E-05 2.4871826E-03 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 02:10:59 3.650u 0.229s 0:04.55 85.0% 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 02:10:59 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1859 !!! WARNING: HIR 75 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.842587 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): 87.55900 139.6330 ymin,ymax (A): 78.79100 116.4830 zmin,zma (A): -4.488000 53.47400 x,y,z range (A): 52.07401 37.69200 57.96200 scale (grids/A): 1.842587 object centre (A): 113.5960 97.63700 24.49300 number of atom coordinates read : 1859 total number of charged atoms : 1723 net assigned charge : 6.514015 assigned positive charge : 271.0462 centred at (gu) : 85.37876 90.95257 91.61831 assigned negative charge : -264.5324 centred at (gu) : 85.71260 90.96442 91.83708 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 50314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20547 grid for indexing accessible points = 1.400000 m= 16182 mr = 30599 m= 2267 mr = 10292 m= 109 mr = 1058 m= 3 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 26908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 13482 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) : 0.6141955 object centre at (A) : 113.5960 97.63700 24.49300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8240480E-02 1.6326934E-02 midg,1,midg; midg,igrid,midg 7.2886334E-03 9.4716586E-03 1,midg,midg; igrid,midg,midg 1.5791671E-02 -1.5000782E-02 gauss-seidel spectral radius is 0.9984863 estimated iterations to convergence 204 setup time was (sec) 0.4800000 now iterating at: 02:11:00 rms-change max change #iterations 3.224771 188.9409 at 10iterations 1.437245 63.40006 at 20iterations 0.6428341 27.86326 at 30iterations 0.2885700 11.01744 at 40iterations 0.1291272 5.474679 at 50iterations 5.7865284E-02 2.321287 at 60iterations 2.5949428E-02 1.025847 at 70iterations 1.1628988E-02 0.4588356 at 80iterations 5.2323183E-03 0.2036722 at 90iterations 2.3648113E-03 9.2502594E-02 at 100iterations 1.0651739E-03 4.1160583E-02 at 110iterations 4.8309614E-04 1.8408775E-02 at 120iterations finished qdiffx linear iterations at : 02:11:07 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 4.8309614E-04 1.8408775E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 02:11:07 7.715u 0.227s 0:08.27 95.8% 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 02:11:07 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1859 !!! WARNING: HIR 75 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.763880 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): 87.55900 139.6330 ymin,ymax (A): 78.79100 116.4830 zmin,zma (A): -4.488000 53.47400 x,y,z range (A): 52.07401 37.69200 57.96200 scale (grids/A): 2.763880 object centre (A): 113.5960 97.63700 24.49300 number of atom coordinates read : 1859 total number of charged atoms : 1723 net assigned charge : 6.514015 assigned positive charge : 271.0462 centred at (gu) : 83.06817 91.42887 92.42751 assigned negative charge : -264.5324 centred at (gu) : 83.56895 91.44668 92.75565 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 116275 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20547 grid for indexing accessible points = 1.400000 m= 52337 mr = 75451 m= 17514 mr = 39174 m= 3878 mr = 12511 m= 459 mr = 2447 m= 24 mr = 213 m= 0 mr = 7 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 60684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 13780 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) : 1.842587 object centre at (A) : 113.5960 97.63700 24.49300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3245870 0.3079890 midg,1,midg; midg,igrid,midg 7.1864784E-02 8.9243501E-02 1,midg,midg; igrid,midg,midg 0.1383410 -0.2831246 gauss-seidel spectral radius is 0.9992218 estimated iterations to convergence 283 setup time was (sec) 0.9300000 now iterating at: 02:11:09 rms-change max change #iterations 7.945757 395.8577 at 10iterations 4.649529 138.3445 at 20iterations 2.695126 89.46519 at 30iterations 1.552143 43.45956 at 40iterations 0.8890861 24.42367 at 50iterations 0.5081769 12.21082 at 60iterations 0.2897119 7.202850 at 70iterations 0.1646227 4.045596 at 80iterations 9.3951091E-02 2.332951 at 90iterations 5.3416323E-02 1.443573 at 100iterations 3.0268269E-02 0.7125988 at 110iterations 1.7165063E-02 0.3993106 at 120iterations 9.7463960E-03 0.2172927 at 130iterations 5.5287150E-03 0.1297321 at 140iterations 3.1343675E-03 8.2714081E-02 at 150iterations 1.7851605E-03 4.1292191E-02 at 160iterations 1.0161537E-03 2.6062012E-02 at 170iterations 5.8194931E-04 1.3719559E-02 at 180iterations finished qdiffx linear iterations at : 02:11:20 total time elapsed so far: 11.86000 # loops : 180 mean,max change (kT/e) : 5.8194931E-04 1.3719559E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.01000 DelPhi exited at 02:11:20 12.012u 0.245s 0:12.64 96.9% 0+0k 0+0io 0pf+0w