Tue Oct 11 07:34:02 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 Tue Oct 11 2011 at 07:34:02 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3297 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6091717 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): 75.47100 125.3930 ymin,ymax (A): -8.514999 48.89900 zmin,zma (A): -2.270000 56.17000 x,y,z range (A): 49.92200 57.41400 58.44000 scale (grids/A): 0.6091717 object centre (A): 100.4320 20.19200 26.95000 number of atom coordinates read : 3297 total number of charged atoms : 3145 net assigned charge : 0.4000100 assigned positive charge : 496.8107 centred at (gu) : 90.59520 89.56189 89.20927 assigned negative charge : -496.4118 centred at (gu) : 90.70017 89.48604 89.23405 start vw surface at 0.1700000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7922 nv = 96 ne = 84 npr = 69020 no. pairs analyzed = 69020 no. exposed pairs = 3699 no. arc points = 25321 no. surface atoms = 1267 nbur = 2030 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 4656 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 0.4100000 number of dielectric boundary points 3610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2595 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 10018 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1702973E-09 -1.0388346E-09 midg,1,midg; midg,igrid,midg -4.9016520E-09 4.4611537E-09 1,midg,midg; igrid,midg,midg 5.8430558E-09 -7.1845347E-09 gauss-seidel spectral radius is 0.9860986 estimated iterations to convergence 69 setup time was (sec) 0.6700000 now iterating at: 07:34:03 rms-change max change #iterations 0.1323313 20.20584 at 10iterations 1.2232450E-02 1.842528 at 20iterations 1.3508394E-03 0.1713562 at 30iterations 2.5321884E-04 3.9144516E-02 at 40iterations 6.4475811E-05 1.0074615E-02 at 50iterations finished qdiffx linear iterations at : 07:34:07 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 6.4475811E-05 1.0074615E-02 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 07:34:07 4.117u 0.290s 0:04.76 92.4% 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 Tue Oct 11 2011 at 07:34:07 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3297 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.827515 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): 75.47100 125.3930 ymin,ymax (A): -8.514999 48.89900 zmin,zma (A): -2.270000 56.17000 x,y,z range (A): 49.92200 57.41400 58.44000 scale (grids/A): 1.827515 object centre (A): 100.4320 20.19200 26.95000 number of atom coordinates read : 3297 total number of charged atoms : 3145 net assigned charge : 0.4000100 assigned positive charge : 496.8107 centred at (gu) : 91.78459 88.68503 87.62678 assigned negative charge : -496.4118 centred at (gu) : 92.09998 88.45760 87.70152 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 87738 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25321 grid for indexing accessible points = 1.400000 m= 30919 mr = 63719 m= 4141 mr = 23347 m= 186 mr = 2525 m= 3 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 3630 time to turn everything in is 0.7500000 number of dielectric boundary points 33325 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 201 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 24629 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) : 0.6091717 object centre at (A) : 100.4320 20.19200 26.95000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5391698E-03 1.0248087E-02 midg,1,midg; midg,igrid,midg -1.1852190E-02 9.2070531E-03 1,midg,midg; igrid,midg,midg 1.6612090E-02 -1.5806234E-02 gauss-seidel spectral radius is 0.9985809 estimated iterations to convergence 210 setup time was (sec) 1.040000 now iterating at: 07:34:08 rms-change max change #iterations 4.490560 168.9639 at 10iterations 2.075879 74.15326 at 20iterations 0.9570057 30.59649 at 30iterations 0.4450183 13.19428 at 40iterations 0.2055218 6.073079 at 50iterations 9.4877325E-02 2.750434 at 60iterations 4.3991964E-02 1.376159 at 70iterations 2.0363048E-02 0.6049957 at 80iterations 9.4246371E-03 0.2669048 at 90iterations 4.3905363E-03 0.1195517 at 100iterations 2.0578138E-03 6.2388420E-02 at 110iterations 9.6374715E-04 2.9926300E-02 at 120iterations finished qdiffx linear iterations at : 07:34:17 total time elapsed so far: 9.390000 # loops : 120 mean,max change (kT/e) : 9.6374715E-04 2.9926300E-02 energy calculations done at 9.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.560000 DelPhi exited at 07:34:17 9.562u 0.315s 0:10.18 96.9% 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 Tue Oct 11 2011 at 07:34:17 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3297 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.741273 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): 75.47100 125.3930 ymin,ymax (A): -8.514999 48.89900 zmin,zma (A): -2.270000 56.17000 x,y,z range (A): 49.92200 57.41400 58.44000 scale (grids/A): 2.741273 object centre (A): 100.4320 20.19200 26.95000 number of atom coordinates read : 3297 total number of charged atoms : 3145 net assigned charge : 0.4000100 assigned positive charge : 496.8107 centred at (gu) : 92.67670 88.02740 86.43993 assigned negative charge : -496.4118 centred at (gu) : 93.14986 87.68628 86.55220 start vw surface at 0.1800000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 203693 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25321 grid for indexing accessible points = 1.400000 m= 103163 mr = 154055 m= 34432 mr = 86249 m= 7185 mr = 27923 m= 854 mr = 5351 m= 45 mr = 569 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 12063 time to turn everything in is 1.940000 number of dielectric boundary points 75210 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 25158 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) : 1.827515 object centre at (A) : 100.4320 20.19200 26.95000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1460262 0.1566736 midg,1,midg; midg,igrid,midg 2.7035614E-02 9.0598471E-02 1,midg,midg; igrid,midg,midg 0.1813820 -0.1826705 gauss-seidel spectral radius is 0.9992498 estimated iterations to convergence 288 setup time was (sec) 2.260000 now iterating at: 07:34:20 rms-change max change #iterations 10.65579 395.9006 at 10iterations 6.200053 139.8943 at 20iterations 3.584338 66.98595 at 30iterations 2.065708 37.89169 at 40iterations 1.190171 21.55853 at 50iterations 0.6838823 11.56899 at 60iterations 0.3923154 7.325156 at 70iterations 0.2252242 4.010117 at 80iterations 0.1291297 2.357468 at 90iterations 7.4155606E-02 1.320854 at 100iterations 4.2494338E-02 0.7469826 at 110iterations 2.4388256E-02 0.3964252 at 120iterations 1.3976358E-02 0.2707062 at 130iterations 8.0413669E-03 0.1349297 at 140iterations 4.6370570E-03 8.5947037E-02 at 150iterations 2.6880344E-03 4.6637058E-02 at 160iterations 1.5721046E-03 2.6391983E-02 at 170iterations 9.3287620E-04 1.6675949E-02 at 180iterations finished qdiffx linear iterations at : 07:34:34 total time elapsed so far: 16.10000 # loops : 180 mean,max change (kT/e) : 9.3287620E-04 1.6675949E-02 energy calculations done at 16.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.28000 DelPhi exited at 07:34:34 16.282u 0.302s 0:17.11 96.9% 0+0k 0+0io 0pf+0w