Sat Oct 8 14:26:36 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 8 2011 at 14:26:36 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6397010 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): -12.45700 43.19400 ymin,ymax (A): -23.76000 22.96500 zmin,zma (A): -7.261000 47.88200 x,y,z range (A): 55.65100 46.72500 55.14300 scale (grids/A): 0.6397010 object centre (A): 15.36850 -0.3975000 20.31050 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : 1.4008060E-02 assigned positive charge : 457.8376 centred at (gu) : 88.74847 89.94942 91.46684 assigned negative charge : -457.8243 centred at (gu) : 88.74164 89.85201 91.37409 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8165 nv = 96 ne = 84 npr = 64361 no. pairs analyzed = 64361 no. exposed pairs = 3430 no. arc points = 24161 no. surface atoms = 1172 nbur = 1868 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 397 mr = 4760 m= 1 mr = 41 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 0.2300000 number of dielectric boundary points 3762 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2337 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 10028 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.3865697E-09 1.7036188E-08 midg,1,midg; midg,igrid,midg -1.3694673E-08 1.2811517E-08 1,midg,midg; igrid,midg,midg -1.4276618E-09 5.9017585E-10 gauss-seidel spectral radius is 0.9873707 estimated iterations to convergence 73 setup time was (sec) 0.4400000 now iterating at: 14:26:36 rms-change max change #iterations 0.1599782 20.38594 at 10iterations 1.6172688E-02 2.159458 at 20iterations 1.6517651E-03 0.2172432 at 30iterations 1.8653968E-04 2.2437096E-02 at 40iterations 2.5569732E-05 3.5171509E-03 at 50iterations finished qdiffx linear iterations at : 14:26:40 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 2.5569732E-05 3.5171509E-03 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 14:26:40 3.667u 0.226s 0:04.16 93.2% 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 8 2011 at 14:26:40 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.919103 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): -12.45700 43.19400 ymin,ymax (A): -23.76000 22.96500 zmin,zma (A): -7.261000 47.88200 x,y,z range (A): 55.65100 46.72500 55.14300 scale (grids/A): 1.919103 object centre (A): 15.36850 -0.3975000 20.31050 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : 1.4008060E-02 assigned positive charge : 457.8376 centred at (gu) : 86.24457 89.84766 94.39977 assigned negative charge : -457.8243 centred at (gu) : 86.22491 89.55578 94.12217 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 89327 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24161 grid for indexing accessible points = 1.400000 m= 32371 mr = 64486 m= 4721 mr = 24366 m= 281 mr = 2868 m= 1 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 106 time to turn everything in is 0.4400000 number of dielectric boundary points 34883 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 22797 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) : 0.6397010 object centre at (A) : 15.36850 -0.3975000 20.31050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3510827E-02 2.4220008E-02 midg,1,midg; midg,igrid,midg -1.5740747E-04 2.3617446E-02 1,midg,midg; igrid,midg,midg -3.2542042E-02 9.9933362E-03 gauss-seidel spectral radius is 0.9986890 estimated iterations to convergence 219 setup time was (sec) 0.6900000 now iterating at: 14:26:41 rms-change max change #iterations 4.742381 274.1958 at 10iterations 2.267832 71.96310 at 20iterations 1.079094 31.09033 at 30iterations 0.5126502 13.87464 at 40iterations 0.2448187 7.026651 at 50iterations 0.1167558 3.641973 at 60iterations 5.5404913E-02 1.612343 at 70iterations 2.6417039E-02 0.7309183 at 80iterations 1.2560754E-02 0.3484688 at 90iterations 5.9929015E-03 0.1743565 at 100iterations 2.8570225E-03 8.0535889E-02 at 110iterations 1.3658191E-03 3.9636135E-02 at 120iterations finished qdiffx linear iterations at : 14:26:49 total time elapsed so far: 8.420000 # loops : 120 mean,max change (kT/e) : 1.3658191E-03 3.9636135E-02 energy calculations done at 8.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.560000 DelPhi exited at 14:26:49 8.558u 0.226s 0:09.11 96.2% 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 8 2011 at 14:26:49 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3040 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.878654 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): -12.45700 43.19400 ymin,ymax (A): -23.76000 22.96500 zmin,zma (A): -7.261000 47.88200 x,y,z range (A): 55.65100 46.72500 55.14300 scale (grids/A): 2.878654 object centre (A): 15.36850 -0.3975000 20.31050 number of atom coordinates read : 3040 total number of charged atoms : 2893 net assigned charge : 1.4008060E-02 assigned positive charge : 457.8376 centred at (gu) : 84.36673 89.77137 96.59946 assigned negative charge : -457.8243 centred at (gu) : 84.33725 89.33364 96.18318 start vw surface at 0.1000000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 206868 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24161 grid for indexing accessible points = 1.400000 m= 105654 mr = 155497 m= 37027 mr = 88025 m= 8424 mr = 29952 m= 1223 mr = 6274 m= 65 mr = 795 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 444 time to turn everything in is 1.180000 number of dielectric boundary points 78689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 23144 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) : 1.919103 object centre at (A) : 15.36850 -0.3975000 20.31050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1058720 0.3505719 midg,1,midg; midg,igrid,midg -4.1118450E-03 0.2550504 1,midg,midg; igrid,midg,midg -0.4722880 0.1534476 gauss-seidel spectral radius is 0.9992762 estimated iterations to convergence 293 setup time was (sec) 1.450000 now iterating at: 14:26:51 rms-change max change #iterations 11.04871 400.9613 at 10iterations 6.500909 142.7459 at 20iterations 3.803560 68.07985 at 30iterations 2.219526 43.53872 at 40iterations 1.290238 25.51557 at 50iterations 0.7509653 14.94944 at 60iterations 0.4360320 7.531731 at 70iterations 0.2529083 4.324203 at 80iterations 0.1467290 2.832550 at 90iterations 8.5034527E-02 1.377045 at 100iterations 4.9259722E-02 0.7831697 at 110iterations 2.8497441E-02 0.4869471 at 120iterations 1.6560813E-02 0.2617042 at 130iterations 9.6069928E-03 0.1638870 at 140iterations 5.5710296E-03 9.1011047E-02 at 150iterations 3.2352023E-03 5.6957245E-02 at 160iterations 1.8845024E-03 3.4057617E-02 at 170iterations 1.1049560E-03 1.9880295E-02 at 180iterations finished qdiffx linear iterations at : 14:27:03 total time elapsed so far: 13.94000 # loops : 180 mean,max change (kT/e) : 1.1049560E-03 1.9880295E-02 energy calculations done at 13.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.07000 DelPhi exited at 14:27:04 14.076u 0.253s 0:14.59 98.1% 0+0k 0+0io 0pf+0w