Sat Oct 8 20:30:10 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 20:30:10 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7156642 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): -24.88200 24.11900 ymin,ymax (A): -13.99700 35.46800 zmin,zma (A): -40.31100 9.433000 x,y,z range (A): 49.00100 49.46500 49.74400 scale (grids/A): 0.7156642 object centre (A): -0.3815002 10.73550 -15.43900 number of atom coordinates read : 2581 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 393.3700 centred at (gu) : 88.15347 88.67047 89.46002 assigned negative charge : -389.9226 centred at (gu) : 88.04238 88.53997 89.55705 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8983 nv = 96 ne = 84 npr = 53723 no. pairs analyzed = 53723 no. exposed pairs = 2972 no. arc points = 21133 no. surface atoms = 1005 nbur = 1576 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 635 mr = 5321 m= 3 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 277 time to turn everything in is 0.3000000 number of dielectric boundary points 4149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1868 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2071389E-07 -3.0546339E-08 midg,1,midg; midg,igrid,midg -7.8194496E-08 1.0274915E-07 1,midg,midg; igrid,midg,midg -6.5938451E-08 8.3372207E-08 gauss-seidel spectral radius is 0.9898704 estimated iterations to convergence 81 setup time was (sec) 0.5200000 now iterating at: 20:30:10 rms-change max change #iterations 0.2371259 28.65372 at 10iterations 3.0590465E-02 3.550949 at 20iterations 3.9143208E-03 0.5243645 at 30iterations 4.9093063E-04 6.3982010E-02 at 40iterations 6.2522180E-05 8.0761909E-03 at 50iterations finished qdiffx linear iterations at : 20:30:13 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 6.2522180E-05 8.0761909E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 20:30:13 3.113u 0.161s 0:03.55 92.1% 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 8 2011 at 20:30:13 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.146993 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): -24.88200 24.11900 ymin,ymax (A): -13.99700 35.46800 zmin,zma (A): -40.31100 9.433000 x,y,z range (A): 49.00100 49.46500 49.74400 scale (grids/A): 2.146993 object centre (A): -0.3815002 10.73550 -15.43900 number of atom coordinates read : 2581 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 393.3700 centred at (gu) : 84.45991 86.01092 88.37949 assigned negative charge : -389.9226 centred at (gu) : 84.12716 85.61976 88.67106 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 94769 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21133 grid for indexing accessible points = 1.400000 m= 39609 mr = 67698 m= 8555 mr = 31309 m= 940 mr = 6221 m= 21 mr = 555 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 7576 time to turn everything in is 0.6600000 number of dielectric boundary points 38111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19459 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) : 0.7156642 object centre at (A) : -0.3815002 10.73550 -15.43900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3579076E-02 4.9421922E-03 midg,1,midg; midg,igrid,midg -3.9142754E-02 2.1977328E-02 1,midg,midg; igrid,midg,midg -1.9099323E-02 9.2312023E-02 gauss-seidel spectral radius is 0.9988985 estimated iterations to convergence 238 setup time was (sec) 0.9200000 now iterating at: 20:30:14 rms-change max change #iterations 5.367415 203.7775 at 10iterations 2.690716 80.49816 at 20iterations 1.362466 36.23500 at 30iterations 0.6920695 19.64119 at 40iterations 0.3487115 9.517515 at 50iterations 0.1764342 4.598718 at 60iterations 8.9460015E-02 2.699901 at 70iterations 4.5372859E-02 1.306494 at 80iterations 2.3012418E-02 0.6366444 at 90iterations 1.1607263E-02 0.2919941 at 100iterations 5.8938996E-03 0.1786301 at 110iterations 2.9829785E-03 7.7441216E-02 at 120iterations finished qdiffx linear iterations at : 20:30:20 total time elapsed so far: 6.940000 # loops : 120 mean,max change (kT/e) : 2.9829785E-03 7.7441216E-02 energy calculations done at 6.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 20:30:21 7.107u 0.193s 0:07.59 96.0% 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 Sat Oct 8 2011 at 20:30:21 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2581 !!! WARNING: GLM 92 has a net charge of -0.0940 !!! WARNING: HIR 94 has a net charge of 0.5140 !!! WARNING: HIR 96 has a net charge of 0.5140 !!! WARNING: HIR 119 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: 3.220489 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): -24.88200 24.11900 ymin,ymax (A): -13.99700 35.46800 zmin,zma (A): -40.31100 9.433000 x,y,z range (A): 49.00100 49.46500 49.74400 scale (grids/A): 3.220489 object centre (A): -0.3815002 10.73550 -15.43900 number of atom coordinates read : 2581 total number of charged atoms : 2449 net assigned charge : 3.448008 assigned positive charge : 393.3700 centred at (gu) : 81.68972 84.01640 87.56916 assigned negative charge : -389.9226 centred at (gu) : 81.19063 83.42962 88.00658 start vw surface at 0.1400000 fill in re-entrant regions at 0.9600000 boundary points on vw surface= 218083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21133 grid for indexing accessible points = 1.400000 m= 120814 mr = 162241 m= 53210 mr = 102795 m= 16640 mr = 45254 m= 3755 mr = 13482 m= 571 mr = 3009 m= 17 mr = 403 m= 0 mr = 3 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 25357 time to turn everything in is 2.130000 number of dielectric boundary points 85903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.250000 number of grid points assigned charge 19592 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) : 2.146993 object centre at (A) : -0.3815002 10.73550 -15.43900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8200834E-02 0.5187359 midg,1,midg; midg,igrid,midg -0.3916817 0.1313584 1,midg,midg; igrid,midg,midg -0.1508077 1.362050 gauss-seidel spectral radius is 0.9993207 estimated iterations to convergence 303 setup time was (sec) 2.420000 now iterating at: 20:30:24 rms-change max change #iterations 11.65785 335.2176 at 10iterations 6.884733 115.7037 at 20iterations 4.066020 67.79284 at 30iterations 2.389956 37.45900 at 40iterations 1.412401 22.77256 at 50iterations 0.8314045 13.07970 at 60iterations 0.4896778 7.095971 at 70iterations 0.2877745 4.323174 at 80iterations 0.1695209 2.796684 at 90iterations 9.9623531E-02 1.602385 at 100iterations 5.8525085E-02 0.8677788 at 110iterations 3.4549024E-02 0.5189419 at 120iterations 2.0316195E-02 0.3484421 at 130iterations 1.1953638E-02 0.1810951 at 140iterations 7.0131761E-03 0.1104355 at 150iterations 4.1300333E-03 5.8630466E-02 at 160iterations 2.4312832E-03 3.6401749E-02 at 170iterations 1.4287224E-03 2.2403717E-02 at 180iterations finished qdiffx linear iterations at : 20:30:33 total time elapsed so far: 12.08000 # loops : 180 mean,max change (kT/e) : 1.4287224E-03 2.2403717E-02 energy calculations done at 12.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.26000 DelPhi exited at 20:30:34 12.258u 0.181s 0:12.71 97.7% 0+0k 0+0io 0pf+0w