Sat Oct 15 11:26:19 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+sph.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 = amb.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 11:26:19 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 430 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7008702 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): -5.639000 43.83600 ymin,ymax (A): -2.979000 47.81500 zmin,zma (A): -7.982000 40.35900 x,y,z range (A): 49.47500 50.79400 48.34100 scale (grids/A): 0.7008702 object centre (A): 19.09850 22.41800 16.18850 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 393.3950 centred at (gu) : 88.37043 91.86562 90.58141 assigned negative charge : -389.1955 centred at (gu) : 88.24778 91.97778 90.52551 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8704 nv = 96 ne = 84 npr = 54610 no. pairs analyzed = 54610 no. exposed pairs = 2995 no. arc points = 21584 no. surface atoms = 1006 nbur = 1600 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 597 mr = 5108 m= 3 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 397 time to turn everything in is 0.2100000 number of dielectric boundary points 4063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1959 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9795 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6205280E-09 6.9238745E-08 midg,1,midg; midg,igrid,midg 6.3219538E-08 -4.1176214E-08 1,midg,midg; igrid,midg,midg -4.7009330E-08 7.0081576E-08 gauss-seidel spectral radius is 0.9894418 estimated iterations to convergence 79 setup time was (sec) 0.4400000 now iterating at: 11:26:20 rms-change max change #iterations 0.2172929 31.78513 at 10iterations 2.6532125E-02 3.429737 at 20iterations 3.1764130E-03 0.4239902 at 30iterations 3.8987049E-04 5.2673340E-02 at 40iterations 4.9064427E-05 5.6762695E-03 at 50iterations finished qdiffx linear iterations at : 11:26:23 total time elapsed so far: 3.800000 # loops : 50 mean,max change (kT/e) : 4.9064427E-05 5.6762695E-03 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.940000 DelPhi exited at 11:26:24 3.945u 0.238s 0:04.70 88.7% 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 Sat Oct 15 2011 at 11:26:24 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 430 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.102611 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): -5.639000 43.83600 ymin,ymax (A): -2.979000 47.81500 zmin,zma (A): -7.982000 40.35900 x,y,z range (A): 49.47500 50.79400 48.34100 scale (grids/A): 2.102611 object centre (A): 19.09850 22.41800 16.18850 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 393.3950 centred at (gu) : 85.11086 95.59623 91.74361 assigned negative charge : -389.1955 centred at (gu) : 84.74319 95.93317 91.57616 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 91777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21584 grid for indexing accessible points = 1.400000 m= 37796 mr = 65320 m= 7821 mr = 29438 m= 727 mr = 5526 m= 19 mr = 437 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 9199 time to turn everything in is 0.4900000 number of dielectric boundary points 37419 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 19564 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) : 0.7008702 object centre at (A) : 19.09850 22.41800 16.18850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5842706E-03 2.4315400E-02 midg,1,midg; midg,igrid,midg 2.6418841E-03 -2.9181357E-02 1,midg,midg; igrid,midg,midg -1.1944012E-02 9.2205748E-02 gauss-seidel spectral radius is 0.9988595 estimated iterations to convergence 234 setup time was (sec) 0.7700000 now iterating at: 11:26:25 rms-change max change #iterations 5.147463 214.9524 at 10iterations 2.555520 77.06886 at 20iterations 1.277987 37.80500 at 30iterations 0.6360875 19.72177 at 40iterations 0.3192036 9.336857 at 50iterations 0.1595400 4.269068 at 60iterations 7.9736181E-02 2.315411 at 70iterations 3.9962038E-02 1.154575 at 80iterations 2.0009998E-02 0.5238419 at 90iterations 9.9923993E-03 0.2854538 at 100iterations 5.0014360E-03 0.1481018 at 110iterations 2.5041914E-03 6.7523956E-02 at 120iterations finished qdiffx linear iterations at : 11:26:33 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 2.5041914E-03 6.7523956E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.550000 DelPhi exited at 11:26:34 9.550u 0.310s 0:10.36 95.1% 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 11:26:34 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2606 !!! WARNING: HIY 36 has a net charge of 0.2000 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN4 430 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.153916 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): -5.639000 43.83600 ymin,ymax (A): -2.979000 47.81500 zmin,zma (A): -7.982000 40.35900 x,y,z range (A): 49.47500 50.79400 48.34100 scale (grids/A): 3.153916 object centre (A): 19.09850 22.41800 16.18850 number of atom coordinates read : 2606 total number of charged atoms : 2466 net assigned charge : 4.200010 assigned positive charge : 393.3950 centred at (gu) : 82.66609 98.39445 92.61532 assigned negative charge : -389.1955 centred at (gu) : 82.11469 98.89969 92.36412 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 211427 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21584 grid for indexing accessible points = 1.400000 m= 116326 mr = 156610 m= 49605 mr = 98253 m= 15187 mr = 41805 m= 3126 mr = 12186 m= 397 mr = 2416 m= 11 mr = 268 m= 0 mr = 4 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 30951 time to turn everything in is 1.530000 number of dielectric boundary points 84537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 19728 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) : 2.102611 object centre at (A) : 19.09850 22.41800 16.18850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2140040 0.2009897 midg,1,midg; midg,igrid,midg -5.7224706E-02 -0.2368604 1,midg,midg; igrid,midg,midg -0.1712005 1.336633 gauss-seidel spectral radius is 0.9993109 estimated iterations to convergence 301 setup time was (sec) 1.830000 now iterating at: 11:26:36 rms-change max change #iterations 11.38893 410.4913 at 10iterations 6.723401 141.4509 at 20iterations 3.962317 76.38338 at 30iterations 2.329357 48.29737 at 40iterations 1.373695 25.70368 at 50iterations 0.8080419 12.72792 at 60iterations 0.4755964 7.777124 at 70iterations 0.2791065 4.724455 at 80iterations 0.1634652 2.623820 at 90iterations 9.5975526E-02 1.434860 at 100iterations 5.6366280E-02 0.9017582 at 110iterations 3.3037379E-02 0.5337791 at 120iterations 1.9395616E-02 0.3131981 at 130iterations 1.1373863E-02 0.1743951 at 140iterations 6.6728075E-03 0.1023264 at 150iterations 3.9179861E-03 5.9474945E-02 at 160iterations 2.2982054E-03 3.7957370E-02 at 170iterations 1.3483220E-03 2.1887779E-02 at 180iterations finished qdiffx linear iterations at : 11:26:50 total time elapsed so far: 15.60000 # loops : 180 mean,max change (kT/e) : 1.3483220E-03 2.1887779E-02 energy calculations done at 15.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.73000 DelPhi exited at 11:26:51 15.734u 0.311s 0:16.74 95.8% 0+0k 0+0io 0pf+0w