Sat Oct 8 18:52:03 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 18:52:03 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2598 !!! 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 496 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6309372 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): -31.84700 17.50700 ymin,ymax (A): -23.68200 22.56500 zmin,zma (A): -12.08600 44.33800 x,y,z range (A): 49.35400 46.24700 56.42400 scale (grids/A): 0.6309372 object centre (A): -7.170000 -0.5584993 16.12600 number of atom coordinates read : 2598 total number of charged atoms : 2488 net assigned charge : 4.500006 assigned positive charge : 398.4570 centred at (gu) : 88.56517 89.36422 89.85871 assigned negative charge : -393.9575 centred at (gu) : 88.46922 89.39841 89.74326 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6877 nv = 96 ne = 84 npr = 53165 no. pairs analyzed = 53165 no. exposed pairs = 3056 no. arc points = 21661 no. surface atoms = 1032 nbur = 1566 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 348 mr = 3856 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 119 time to turn everything in is 0.3000000 number of dielectric boundary points 3317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2178 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8362 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7691940E-09 1.5175413E-08 midg,1,midg; midg,igrid,midg 9.5141415E-09 1.7823375E-09 1,midg,midg; igrid,midg,midg -5.2823732E-09 1.0209818E-08 gauss-seidel spectral radius is 0.9869848 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 18:52:04 rms-change max change #iterations 0.1391482 22.12878 at 10iterations 1.3415597E-02 2.365505 at 20iterations 1.2632225E-03 0.1982346 at 30iterations 1.2239059E-04 1.7826080E-02 at 40iterations 1.1928068E-05 1.5602112E-03 at 50iterations finished qdiffx linear iterations at : 18:52:07 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 1.1928068E-05 1.5602112E-03 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 18:52:08 4.484u 0.282s 0:05.06 94.0% 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 18:52:08 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2598 !!! 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 496 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.892811 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): -31.84700 17.50700 ymin,ymax (A): -23.68200 22.56500 zmin,zma (A): -12.08600 44.33800 x,y,z range (A): 49.35400 46.24700 56.42400 scale (grids/A): 1.892811 object centre (A): -7.170000 -0.5584993 16.12600 number of atom coordinates read : 2598 total number of charged atoms : 2488 net assigned charge : 4.500006 assigned positive charge : 398.4570 centred at (gu) : 85.69526 88.09223 89.57566 assigned negative charge : -393.9575 centred at (gu) : 85.40746 88.19486 89.22961 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74299 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21661 grid for indexing accessible points = 1.400000 m= 27210 mr = 52201 m= 4023 mr = 20463 m= 236 mr = 2524 m= 3 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 3852 time to turn everything in is 0.5700000 number of dielectric boundary points 30476 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 19571 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) : 0.6309372 object centre at (A) : -7.170000 -0.5584993 16.12600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1387104E-02 3.5419792E-02 midg,1,midg; midg,igrid,midg 1.3918226E-02 1.7923960E-03 1,midg,midg; igrid,midg,midg -2.2665525E-03 3.9641321E-02 gauss-seidel spectral radius is 0.9986163 estimated iterations to convergence 213 setup time was (sec) 0.9100000 now iterating at: 18:52:09 rms-change max change #iterations 4.218773 158.2224 at 10iterations 1.970764 67.27094 at 20iterations 0.9160634 30.02616 at 30iterations 0.4269237 13.45927 at 40iterations 0.1998727 6.249744 at 50iterations 9.3176767E-02 2.875118 at 60iterations 4.3404050E-02 1.499398 at 70iterations 2.0268718E-02 0.6790497 at 80iterations 9.4234822E-03 0.3051224 at 90iterations 4.4078347E-03 0.1346779 at 100iterations 2.0637624E-03 6.2237263E-02 at 110iterations 9.5996202E-04 3.4265041E-02 at 120iterations finished qdiffx linear iterations at : 18:52:18 total time elapsed so far: 9.820000 # loops : 120 mean,max change (kT/e) : 9.5996202E-04 3.4265041E-02 energy calculations done at 9.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.05000 DelPhi exited at 18:52:18 10.055u 0.294s 0:10.64 97.1% 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 18:52:19 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2598 !!! 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 496 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.839217 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): -31.84700 17.50700 ymin,ymax (A): -23.68200 22.56500 zmin,zma (A): -12.08600 44.33800 x,y,z range (A): 49.35400 46.24700 56.42400 scale (grids/A): 2.839217 object centre (A): -7.170000 -0.5584993 16.12600 number of atom coordinates read : 2598 total number of charged atoms : 2488 net assigned charge : 4.500006 assigned positive charge : 398.4570 centred at (gu) : 83.54269 87.13811 89.36337 assigned negative charge : -393.9575 centred at (gu) : 83.11125 87.29214 88.84436 start vw surface at 0.1800000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 171825 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21661 grid for indexing accessible points = 1.400000 m= 88432 mr = 126095 m= 31589 mr = 73374 m= 7127 mr = 25546 m= 962 mr = 5436 m= 74 mr = 712 m= 0 mr = 31 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 12964 time to turn everything in is 1.540000 number of dielectric boundary points 68815 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 19904 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) : 1.892811 object centre at (A) : -7.170000 -0.5584993 16.12600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1598828 0.4042494 midg,1,midg; midg,igrid,midg 0.1664185 7.8505659E-03 1,midg,midg; igrid,midg,midg 2.3164447E-02 0.5130007 gauss-seidel spectral radius is 0.9992487 estimated iterations to convergence 288 setup time was (sec) 1.890000 now iterating at: 18:52:21 rms-change max change #iterations 9.899667 374.2282 at 10iterations 5.739646 162.3197 at 20iterations 3.293647 71.80486 at 30iterations 1.891639 42.75219 at 40iterations 1.086211 21.88529 at 50iterations 0.6216034 11.45945 at 60iterations 0.3568895 7.171609 at 70iterations 0.2041129 4.714868 at 80iterations 0.1166310 2.204676 at 90iterations 6.6900924E-02 1.248962 at 100iterations 3.8262393E-02 0.7204332 at 110iterations 2.1869944E-02 0.4098053 at 120iterations 1.2546881E-02 0.2207947 at 130iterations 7.1718101E-03 0.1380711 at 140iterations 4.0976950E-03 7.5596809E-02 at 150iterations 2.3425713E-03 4.4483185E-02 at 160iterations 1.3383782E-03 2.4699211E-02 at 170iterations 7.6662085E-04 1.3352394E-02 at 180iterations finished qdiffx linear iterations at : 18:52:34 total time elapsed so far: 15.27000 # loops : 180 mean,max change (kT/e) : 7.6662085E-04 1.3352394E-02 energy calculations done at 15.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.45000 DelPhi exited at 18:52:35 15.456u 0.309s 0:16.05 98.1% 0+0k 0+0io 0pf+0w