Thu Jan 19 14:04:29 PST 2012 #!/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 Thu Jan 19 2012 at 14:04:33 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: 374 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5443 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: SEP 499 has a net charge of -0.2750 !!! WARNING: ASP 553 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.1761661 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): 192.1630 276.3070 ymin,ymax (A): 63.18600 172.0420 zmin,zma (A): -67.16100 134.9210 x,y,z range (A): 84.14400 108.8560 202.0820 scale (grids/A): 0.1761661 object centre (A): 234.2350 117.6140 33.87999 number of atom coordinates read : 5443 total number of charged atoms : 5240 net assigned charge : -2.379953 assigned positive charge : 810.9777 centred at (gu) : 92.22612 86.87853 77.61938 assigned negative charge : -813.3647 centred at (gu) : 92.25842 86.87775 77.61607 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 594 nv = 96 ne = 84 npr = 109633 no. pairs analyzed = 109633 no. exposed pairs = 7312 no. arc points = 47512 no. surface atoms = 2484 nbur = 2959 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 4.966707 m= 5 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 457 no. dielectric boundary points in salt = 21 no. grid points charged and at boundary= 880 ## 434 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 1057 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4313277E-25 -1.3019558E-35 midg,1,midg; midg,igrid,midg -5.4644230E-29 -3.7538300E-31 1,midg,midg; igrid,midg,midg 9.3576979E-30 -2.8722900E-28 gauss-seidel spectral radius is 0.8510725 estimated iterations to convergence 23 setup time was (sec) 0.5500000 now iterating at: 14:04:37 rms-change max change #iterations 2.0976005E-04 0.2041559 at 10iterations 1.1343648E-05 1.2054443E-02 at 20iterations 6.6163096E-07 7.2193146E-04 at 30iterations 3.9379675E-08 4.2915344E-05 at 40iterations 4.0320969E-09 2.8610229E-06 at 50iterations finished qdiffx linear iterations at : 14:08:29 total time elapsed so far: 77.35000 # loops : 50 mean,max change (kT/e) : 4.0320969E-09 2.8610229E-06 energy calculations done at 77.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 77.48000 DelPhi exited at 14:08:31 77.472u 0.190s 3:58.30 32.5% 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 Thu Jan 19 2012 at 14:08:37 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: 374 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5443 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: SEP 499 has a net charge of -0.2750 !!! WARNING: ASP 553 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5284984 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): 192.1630 276.3070 ymin,ymax (A): 63.18600 172.0420 zmin,zma (A): -67.16100 134.9210 x,y,z range (A): 84.14400 108.8560 202.0820 scale (grids/A): 0.5284984 object centre (A): 234.2350 117.6140 33.87999 number of atom coordinates read : 5443 total number of charged atoms : 5240 net assigned charge : -2.379953 assigned positive charge : 810.9777 centred at (gu) : 96.67651 80.63380 52.85614 assigned negative charge : -813.3647 centred at (gu) : 96.77523 80.63308 52.84780 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 9478 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47512 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 4.633574 m= 374 mr = 4723 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 5118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4592 ## 555 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 12548 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) : 0.1761661 object centre at (A) : 234.2350 117.6140 33.87999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7971572E-05 -2.2463993E-13 midg,1,midg; midg,igrid,midg -3.5210159E-09 7.7307431E-12 1,midg,midg; igrid,midg,midg 2.0255311E-10 -3.2676033E-09 gauss-seidel spectral radius is 0.9815701 estimated iterations to convergence 61 setup time was (sec) 0.4300000 now iterating at: 14:08:42 rms-change max change #iterations 7.9328418E-02 11.10181 at 10iterations 5.0854636E-03 0.7587547 at 20iterations 6.0297112E-04 0.1027036 at 30iterations 2.0230854E-04 3.9661884E-02 at 40iterations 7.7905082E-05 1.5290737E-02 at 50iterations 3.0381732E-05 5.8970451E-03 at 60iterations 1.1919946E-05 2.2778511E-03 at 70iterations 4.6959622E-06 8.8310242E-04 at 80iterations 1.8558100E-06 3.4379959E-04 at 90iterations 7.3862014E-07 1.3351440E-04 at 100iterations 3.0209966E-07 5.3405762E-05 at 110iterations 1.3530217E-07 2.4795532E-05 at 120iterations finished qdiffx linear iterations at : 14:09:36 total time elapsed so far: 18.46000 # loops : 120 mean,max change (kT/e) : 1.3530217E-07 2.4795532E-05 energy calculations done at 18.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.60000 DelPhi exited at 14:09:37 18.601u 0.203s 1:00.60 31.0% 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 Thu Jan 19 2012 at 14:09:44 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: 374 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5443 !!! WARNING: ARG 48 has a net charge of 0.0400 !!! WARNING: ARG 52 has a net charge of 0.0400 !!! WARNING: LYS 138 has a net charge of 0.0200 !!! WARNING: GLN 139 has a net charge of 0.0170 !!! WARNING: ASP 142 has a net charge of -0.2080 !!! WARNING: LYS 155 has a net charge of 0.0200 !!! WARNING: LYS 184 has a net charge of 0.0200 !!! WARNING: LYS 217 has a net charge of 0.0200 !!! WARNING: LYS 286 has a net charge of 0.0200 !!! WARNING: ARG 365 has a net charge of 0.0400 !!! WARNING: GLN 369 has a net charge of 0.0170 !!! WARNING: ASP 385 has a net charge of -0.2080 !!! WARNING: LYS 442 has a net charge of 0.0200 !!! WARNING: GLN 448 has a net charge of 0.0170 !!! WARNING: LYS 454 has a net charge of 0.0200 !!! WARNING: SEP 499 has a net charge of -0.2750 !!! WARNING: ASP 553 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.7927475 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): 192.1630 276.3070 ymin,ymax (A): 63.18600 172.0420 zmin,zma (A): -67.16100 134.9210 x,y,z range (A): 84.14400 108.8560 202.0820 scale (grids/A): 0.7927475 object centre (A): 234.2350 117.6140 33.87999 number of atom coordinates read : 5443 total number of charged atoms : 5240 net assigned charge : -2.379953 assigned positive charge : 810.9777 centred at (gu) : 100.0142 75.95012 34.28380 assigned negative charge : -813.3647 centred at (gu) : 100.1626 75.94954 34.27165 start vw surface at 0.1400000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 23726 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47512 initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 4.573004 m= 2316 mr = 13671 m= 26 mr = 652 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.3300000 number of dielectric boundary points 11745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3009 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 24059 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) : 0.5284984 object centre at (A) : 234.2350 117.6140 33.87999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1130161 -1.2268191E-10 midg,1,midg; midg,igrid,midg -1.9127897E-06 6.8423982E-09 1,midg,midg; igrid,midg,midg 1.0077836E-07 -1.8282149E-06 gauss-seidel spectral radius is 0.9916372 estimated iterations to convergence 89 setup time was (sec) 0.5400000 now iterating at: 14:09:49 rms-change max change #iterations 0.5807283 46.50178 at 10iterations 9.2645638E-02 8.664677 at 20iterations 1.4770309E-02 1.555819 at 30iterations 2.4493979E-03 0.2336769 at 40iterations 5.7069492E-04 5.4903030E-02 at 50iterations 2.5149263E-04 2.2436142E-02 at 60iterations 1.3767194E-04 1.2187958E-02 at 70iterations 7.7149300E-05 6.7520142E-03 at 80iterations 4.3355725E-05 3.7651062E-03 at 90iterations 2.4376783E-05 2.1152496E-03 at 100iterations 1.3704397E-05 1.1944771E-03 at 110iterations 7.7131308E-06 6.7639351E-04 at 120iterations 4.3378500E-06 3.8123131E-04 at 130iterations 2.4450494E-06 2.1600723E-04 at 140iterations 1.3893641E-06 1.2397766E-04 at 150iterations 7.9713237E-07 7.2479248E-05 at 160iterations 4.8164156E-07 4.5776367E-05 at 170iterations 3.2225520E-07 3.3378601E-05 at 180iterations finished qdiffx linear iterations at : 14:10:21 total time elapsed so far: 11.31000 # loops : 180 mean,max change (kT/e) : 3.2225520E-07 3.3378601E-05 energy calculations done at 11.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.44000 DelPhi exited at 14:10:22 11.447u 0.228s 0:38.60 30.2% 0+0k 0+0io 0pf+0w