Sun Oct 9 04:11:37 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 04:11:37 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4848 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.4181201 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): -2.552000 78.88100 ymin,ymax (A): -12.41400 55.74700 zmin,zma (A): -16.72600 68.41700 x,y,z range (A): 81.43301 68.16100 85.14300 scale (grids/A): 0.4181201 object centre (A): 38.16450 21.66650 25.84550 number of atom coordinates read : 4848 total number of charged atoms : 4530 net assigned charge : 23.31397 assigned positive charge : 712.7995 centred at (gu) : 85.54175 91.71355 83.65041 assigned negative charge : -689.4907 centred at (gu) : 85.39265 91.75871 83.51733 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4910 nv = 96 ne = 84 npr = 98371 no. pairs analyzed = 98371 no. exposed pairs = 6356 no. arc points = 44279 no. surface atoms = 2121 nbur = 2727 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.988000 m= 106 mr = 2143 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3294 ## 721 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6614 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4202647E-12 6.6813341E-13 midg,1,midg; midg,igrid,midg 1.8149956E-12 2.5018058E-12 1,midg,midg; igrid,midg,midg -2.3623083E-12 1.2393682E-12 gauss-seidel spectral radius is 0.9708772 estimated iterations to convergence 49 setup time was (sec) 0.5000000 now iterating at: 04:11:38 rms-change max change #iterations 2.5217688E-02 4.918297 at 10iterations 2.7590727E-03 0.4872513 at 20iterations 7.8790396E-04 0.1331692 at 30iterations 2.3318663E-04 3.9224625E-02 at 40iterations 6.9175228E-05 1.1594772E-02 at 50iterations finished qdiffx linear iterations at : 04:11:41 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 6.9175228E-05 1.1594772E-02 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 04:11:41 3.648u 0.180s 0:04.11 92.9% 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 Sun Oct 9 2011 at 04:11:41 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4848 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.254360 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): -2.552000 78.88100 ymin,ymax (A): -12.41400 55.74700 zmin,zma (A): -16.72600 68.41700 x,y,z range (A): 81.43301 68.16100 85.14300 scale (grids/A): 1.254360 object centre (A): 38.16450 21.66650 25.84550 number of atom coordinates read : 4848 total number of charged atoms : 4530 net assigned charge : 23.31397 assigned positive charge : 712.7995 centred at (gu) : 76.62359 95.13885 70.94957 assigned negative charge : -689.4907 centred at (gu) : 76.17720 95.27579 70.55190 start vw surface at 0.1300000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 57625 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44279 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.876000 m= 11992 mr = 36214 m= 489 mr = 6764 m= 4 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 740 time to turn everything in is 0.3200000 number of dielectric boundary points 27046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 792 ## 26 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 30967 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) : 0.4181201 object centre at (A) : 38.16450 21.66650 25.84550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1049279E-02 2.2160250E-03 midg,1,midg; midg,igrid,midg 2.8459271E-03 2.2624058E-03 1,midg,midg; igrid,midg,midg -2.0842953E-04 1.4954485E-03 gauss-seidel spectral radius is 0.9969604 estimated iterations to convergence 145 setup time was (sec) 0.5300000 now iterating at: 04:11:42 rms-change max change #iterations 2.250220 115.5509 at 10iterations 0.7211728 30.82046 at 20iterations 0.2329030 9.800627 at 30iterations 7.6020919E-02 3.555860 at 40iterations 2.5360029E-02 1.067780 at 50iterations 9.0243304E-03 0.3604851 at 60iterations 3.8562277E-03 0.1560888 at 70iterations 2.0718689E-03 7.6484680E-02 at 80iterations 1.2595704E-03 4.1925192E-02 at 90iterations 8.0682099E-04 2.7091980E-02 at 100iterations 5.2285852E-04 1.6794205E-02 at 110iterations 3.4050338E-04 1.0837555E-02 at 120iterations finished qdiffx linear iterations at : 04:11:49 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 3.4050338E-04 1.0837555E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 04:11:50 7.676u 0.218s 0:08.16 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 04:11:50 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: 345 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4848 !!! WARNING: HIR 58 has a net charge of 0.5140 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 2209 has a net charge of 1.4000 !!! WARNING: FE 5 has a net charge of 1.4000 !!! WARNING: FE 6 has a net charge of 1.4000 !!! WARNING: FE 7 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.881541 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): -2.552000 78.88100 ymin,ymax (A): -12.41400 55.74700 zmin,zma (A): -16.72600 68.41700 x,y,z range (A): 81.43301 68.16100 85.14300 scale (grids/A): 1.881541 object centre (A): 38.16450 21.66650 25.84550 number of atom coordinates read : 4848 total number of charged atoms : 4530 net assigned charge : 23.31397 assigned positive charge : 712.7995 centred at (gu) : 69.93491 97.70788 61.42410 assigned negative charge : -689.4907 centred at (gu) : 69.26579 97.91364 60.82772 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 135466 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44279 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.848000 m= 47723 mr = 90899 m= 7550 mr = 34404 m= 433 mr = 4602 m= 9 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2399 time to turn everything in is 0.7200000 number of dielectric boundary points 61126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 35640 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) : 1.254360 object centre at (A) : 38.16450 21.66650 25.84550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3398229 2.9210841E-02 midg,1,midg; midg,igrid,midg 6.7962632E-02 4.3089516E-02 1,midg,midg; igrid,midg,midg 7.0963046E-03 2.1502443E-02 gauss-seidel spectral radius is 0.9986874 estimated iterations to convergence 219 setup time was (sec) 0.9500000 now iterating at: 04:11:51 rms-change max change #iterations 6.921996 222.3273 at 10iterations 3.429215 109.1741 at 20iterations 1.676495 49.84599 at 30iterations 0.8165284 20.99940 at 40iterations 0.3957150 12.17303 at 50iterations 0.1913320 6.072628 at 60iterations 9.2339955E-02 2.439975 at 70iterations 4.4573024E-02 1.236455 at 80iterations 2.1459658E-02 0.5254431 at 90iterations 1.0418564E-02 0.2752228 at 100iterations 5.1229633E-03 0.1307859 at 110iterations 2.5999846E-03 6.8038940E-02 at 120iterations 1.3878226E-03 3.5675049E-02 at 130iterations 8.0269447E-04 2.0309448E-02 at 140iterations 5.0745078E-04 1.2531281E-02 at 150iterations 3.4496177E-04 8.2168579E-03 at 160iterations 2.4611957E-04 5.4798126E-03 at 170iterations 1.7916714E-04 3.7517548E-03 at 180iterations finished qdiffx linear iterations at : 04:12:02 total time elapsed so far: 12.04000 # loops : 180 mean,max change (kT/e) : 1.7916714E-04 3.7517548E-03 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.17000 DelPhi exited at 04:12:02 12.172u 0.205s 0:12.70 97.4% 0+0k 0+0io 0pf+0w