Sun Oct 9 10:17:00 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 Sun Oct 9 2011 at 10:17:00 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2210 !!! WARNING: HIR 524 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: 0.6674040 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): -1.560000 48.38000 ymin,ymax (A): -26.74700 26.45300 zmin,zma (A): -5.406000 47.93500 x,y,z range (A): 49.94000 53.20000 53.34100 scale (grids/A): 0.6674040 object centre (A): 23.41000 -0.1470003 21.26450 number of atom coordinates read : 2210 total number of charged atoms : 2073 net assigned charge : 2.514014 assigned positive charge : 322.2026 centred at (gu) : 90.56484 92.37432 91.08740 assigned negative charge : -319.6893 centred at (gu) : 90.60346 92.22404 91.08895 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 = 43949 no. pairs analyzed = 43949 no. exposed pairs = 2956 no. arc points = 21128 no. surface atoms = 985 nbur = 1225 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3596 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1924 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7722 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9186731E-09 8.3380636E-09 midg,1,midg; midg,igrid,midg -1.3789387E-08 5.9220113E-08 1,midg,midg; igrid,midg,midg 1.2959829E-08 -6.7228412E-10 gauss-seidel spectral radius is 0.9883391 estimated iterations to convergence 76 setup time was (sec) 0.5200000 now iterating at: 10:17:01 rms-change max change #iterations 0.1609692 22.52615 at 10iterations 1.7414907E-02 2.639951 at 20iterations 1.8671949E-03 0.2726899 at 30iterations 1.9721994E-04 3.4369275E-02 at 40iterations 2.1920536E-05 3.2386780E-03 at 50iterations finished qdiffx linear iterations at : 10:17:04 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 2.1920536E-05 3.2386780E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 10:17:04 3.392u 0.191s 0:03.86 92.7% 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 Sun Oct 9 2011 at 10:17:04 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2210 !!! WARNING: HIR 524 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: 2.002212 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): -1.560000 48.38000 ymin,ymax (A): -26.74700 26.45300 zmin,zma (A): -5.406000 47.93500 x,y,z range (A): 49.94000 53.20000 53.34100 scale (grids/A): 2.002212 object centre (A): 23.41000 -0.1470003 21.26450 number of atom coordinates read : 2210 total number of charged atoms : 2073 net assigned charge : 2.514014 assigned positive charge : 322.2026 centred at (gu) : 91.69439 97.12277 93.26206 assigned negative charge : -319.6893 centred at (gu) : 91.81081 96.67260 93.26700 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 72812 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21128 grid for indexing accessible points = 1.400000 m= 26462 mr = 48495 m= 4838 mr = 19334 m= 452 mr = 3286 m= 6 mr = 247 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1083 time to turn everything in is 0.5300000 number of dielectric boundary points 33208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 16407 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) : 0.6674040 object centre at (A) : 23.41000 -0.1470003 21.26450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7843943E-02 5.3565003E-02 midg,1,midg; midg,igrid,midg -4.1255457E-03 6.3117310E-02 1,midg,midg; igrid,midg,midg -1.8444203E-02 -2.7636154E-02 gauss-seidel spectral radius is 0.9987298 estimated iterations to convergence 222 setup time was (sec) 0.8200000 now iterating at: 10:17:05 rms-change max change #iterations 4.189576 180.5628 at 10iterations 2.013764 72.50819 at 20iterations 0.9758449 33.98825 at 30iterations 0.4686700 15.75953 at 40iterations 0.2262651 7.899796 at 50iterations 0.1086958 3.985340 at 60iterations 5.2387342E-02 1.609325 at 70iterations 2.5197713E-02 0.7490444 at 80iterations 1.2105649E-02 0.4381237 at 90iterations 5.8280230E-03 0.1866322 at 100iterations 2.8009301E-03 8.3442688E-02 at 110iterations 1.3556798E-03 4.9132347E-02 at 120iterations finished qdiffx linear iterations at : 10:17:12 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 1.3556798E-03 4.9132347E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 10:17:13 7.694u 0.233s 0:08.20 96.5% 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 Sun Oct 9 2011 at 10:17:13 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2210 !!! WARNING: HIR 524 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: 3.003318 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): -1.560000 48.38000 ymin,ymax (A): -26.74700 26.45300 zmin,zma (A): -5.406000 47.93500 x,y,z range (A): 49.94000 53.20000 53.34100 scale (grids/A): 3.003318 object centre (A): 23.41000 -0.1470003 21.26450 number of atom coordinates read : 2210 total number of charged atoms : 2073 net assigned charge : 2.514014 assigned positive charge : 322.2026 centred at (gu) : 92.54139 100.6841 94.89293 assigned negative charge : -319.6893 centred at (gu) : 92.71625 100.0089 94.90046 start vw surface at 0.1200000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 168194 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21128 grid for indexing accessible points = 1.400000 m= 82981 mr = 118081 m= 32366 mr = 66949 m= 9161 mr = 26144 m= 1962 mr = 7192 m= 195 mr = 1572 m= 1 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 3447 time to turn everything in is 1.310000 number of dielectric boundary points 74835 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 16584 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) : 2.002212 object centre at (A) : 23.41000 -0.1470003 21.26450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1096173 0.6082213 midg,1,midg; midg,igrid,midg -6.9387153E-02 0.4780076 1,midg,midg; igrid,midg,midg -0.2340812 -0.2976316 gauss-seidel spectral radius is 0.9992870 estimated iterations to convergence 295 setup time was (sec) 1.640000 now iterating at: 10:17:14 rms-change max change #iterations 9.693274 412.5834 at 10iterations 5.671522 126.5617 at 20iterations 3.312589 78.12414 at 30iterations 1.940845 35.34303 at 40iterations 1.127553 22.44534 at 50iterations 0.6577463 12.34437 at 60iterations 0.3818344 6.737489 at 70iterations 0.2216081 3.764134 at 80iterations 0.1290040 2.249577 at 90iterations 7.4748933E-02 1.478994 at 100iterations 4.3386467E-02 0.7657928 at 110iterations 2.5217511E-02 0.4269333 at 120iterations 1.4605691E-02 0.2866874 at 130iterations 8.4908484E-03 0.1791557 at 140iterations 4.9291174E-03 0.1003487 at 150iterations 2.8630788E-03 4.8887253E-02 at 160iterations 1.6628449E-03 2.7851105E-02 at 170iterations 9.6726249E-04 1.8894196E-02 at 180iterations finished qdiffx linear iterations at : 10:17:25 total time elapsed so far: 12.21000 # loops : 180 mean,max change (kT/e) : 9.6726249E-04 1.8894196E-02 energy calculations done at 12.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 10:17:26 12.402u 0.244s 0:12.93 97.7% 0+0k 0+0io 0pf+0w