Sat Oct 15 15:29:50 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 Sat Oct 15 2011 at 15:29:50 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIR 71 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: 0.6408756 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): -12.47200 36.76600 ymin,ymax (A): -25.97200 22.32300 zmin,zma (A): -10.13500 45.41400 x,y,z range (A): 49.23800 48.29500 55.54900 scale (grids/A): 0.6408756 object centre (A): 12.14700 -1.824500 17.63950 number of atom coordinates read : 2737 total number of charged atoms : 2588 net assigned charge : 1.514017 assigned positive charge : 418.4677 centred at (gu) : 90.55287 90.38161 91.85915 assigned negative charge : -416.9543 centred at (gu) : 90.31660 90.22614 91.77286 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7415 nv = 96 ne = 84 npr = 56116 no. pairs analyzed = 56116 no. exposed pairs = 3311 no. arc points = 23054 no. surface atoms = 1126 nbur = 1611 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 359 mr = 4135 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3603 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2345 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9056 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2168506E-09 1.9127745E-08 midg,1,midg; midg,igrid,midg -1.6941572E-08 2.3210408E-08 1,midg,midg; igrid,midg,midg -2.5882517E-08 3.5266876E-08 gauss-seidel spectral radius is 0.9873935 estimated iterations to convergence 73 setup time was (sec) 0.5500000 now iterating at: 15:29:51 rms-change max change #iterations 0.1537838 23.11974 at 10iterations 1.5465748E-02 2.319238 at 20iterations 1.6279450E-03 0.2293930 at 30iterations 1.8429324E-04 2.7960777E-02 at 40iterations 2.8021499E-05 3.6163330E-03 at 50iterations finished qdiffx linear iterations at : 15:29:54 total time elapsed so far: 3.810000 # loops : 50 mean,max change (kT/e) : 2.8021499E-05 3.6163330E-03 energy calculations done at 3.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 15:29:55 3.988u 0.419s 0:04.79 91.6% 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 Sat Oct 15 2011 at 15:29:55 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIR 71 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: 1.922627 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): -12.47200 36.76600 ymin,ymax (A): -25.97200 22.32300 zmin,zma (A): -10.13500 45.41400 x,y,z range (A): 49.23800 48.29500 55.54900 scale (grids/A): 1.922627 object centre (A): 12.14700 -1.824500 17.63950 number of atom coordinates read : 2737 total number of charged atoms : 2588 net assigned charge : 1.514017 assigned positive charge : 418.4677 centred at (gu) : 91.65813 91.14420 95.57667 assigned negative charge : -416.9543 centred at (gu) : 90.94964 90.67811 95.31845 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80347 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23054 grid for indexing accessible points = 1.400000 m= 28944 mr = 56611 m= 4395 mr = 21378 m= 224 mr = 2666 m= 1 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 199 time to turn everything in is 0.6600000 number of dielectric boundary points 33180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 173 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 20378 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) : 0.6408756 object centre at (A) : 12.14700 -1.824500 17.63950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8566420E-02 9.2671309E-03 midg,1,midg; midg,igrid,midg -1.4415443E-02 1.2891695E-02 1,midg,midg; igrid,midg,midg -8.1375567E-03 6.5572657E-02 gauss-seidel spectral radius is 0.9986721 estimated iterations to convergence 217 setup time was (sec) 0.9500000 now iterating at: 15:29:56 rms-change max change #iterations 4.578253 178.0910 at 10iterations 2.165096 73.88460 at 20iterations 1.029655 32.86291 at 30iterations 0.4887545 16.06745 at 40iterations 0.2318566 6.956628 at 50iterations 0.1096391 3.466503 at 60iterations 5.2028965E-02 1.576900 at 70iterations 2.4637448E-02 0.7298852 at 80iterations 1.1707442E-02 0.3586807 at 90iterations 5.5546025E-03 0.1763535 at 100iterations 2.6362722E-03 8.4640503E-02 at 110iterations 1.2525909E-03 3.5917282E-02 at 120iterations finished qdiffx linear iterations at : 15:30:05 total time elapsed so far: 9.950000 # loops : 120 mean,max change (kT/e) : 1.2525909E-03 3.5917282E-02 energy calculations done at 9.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.12000 DelPhi exited at 15:30:06 10.127u 0.430s 0:11.11 94.9% 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 Sat Oct 15 2011 at 15:30:06 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2737 !!! WARNING: HIR 71 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: 2.883940 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): -12.47200 36.76600 ymin,ymax (A): -25.97200 22.32300 zmin,zma (A): -10.13500 45.41400 x,y,z range (A): 49.23800 48.29500 55.54900 scale (grids/A): 2.883940 object centre (A): 12.14700 -1.824500 17.63950 number of atom coordinates read : 2737 total number of charged atoms : 2588 net assigned charge : 1.514017 assigned positive charge : 418.4677 centred at (gu) : 92.48698 91.71622 98.36495 assigned negative charge : -416.9543 centred at (gu) : 91.42450 91.01718 97.97753 start vw surface at 0.1300000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 186001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23054 grid for indexing accessible points = 1.400000 m= 94441 mr = 136935 m= 33281 mr = 77629 m= 7528 mr = 26678 m= 971 mr = 5545 m= 48 mr = 618 m= 0 mr = 20 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 658 time to turn everything in is 1.670000 number of dielectric boundary points 74845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 20704 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) : 1.922627 object centre at (A) : 12.14700 -1.824500 17.63950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7083188 0.3049737 midg,1,midg; midg,igrid,midg -0.1344584 0.1433079 1,midg,midg; igrid,midg,midg -2.5962504E-02 0.6223741 gauss-seidel spectral radius is 0.9992664 estimated iterations to convergence 291 setup time was (sec) 2.020000 now iterating at: 15:30:08 rms-change max change #iterations 10.56084 367.8345 at 10iterations 6.194682 121.7938 at 20iterations 3.614077 78.33598 at 30iterations 2.103637 39.28634 at 40iterations 1.219921 23.61003 at 50iterations 0.7082473 13.75739 at 60iterations 0.4095722 8.118561 at 70iterations 0.2370997 4.594015 at 80iterations 0.1375079 2.442673 at 90iterations 7.9456568E-02 1.479797 at 100iterations 4.5922998E-02 0.7831612 at 110iterations 2.6574027E-02 0.5073891 at 120iterations 1.5377634E-02 0.2616301 at 130iterations 8.8880984E-03 0.1452789 at 140iterations 5.1725423E-03 9.3582153E-02 at 150iterations 3.0287884E-03 5.5025816E-02 at 160iterations 1.7867660E-03 3.3185959E-02 at 170iterations 1.0675646E-03 1.9721985E-02 at 180iterations finished qdiffx linear iterations at : 15:30:25 total time elapsed so far: 17.86000 # loops : 180 mean,max change (kT/e) : 1.0675646E-03 1.9721985E-02 energy calculations done at 17.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.02000 DelPhi exited at 15:30:26 18.028u 0.481s 0:20.00 92.5% 0+0k 0+0io 0pf+0w