Sat Oct 8 16:43:48 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 16:43:48 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4568 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5469519 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): 16.92800 78.89300 ymin,ymax (A): 119.1950 184.2830 zmin,zma (A): -1.737000 59.69700 x,y,z range (A): 61.96500 65.08799 61.43400 scale (grids/A): 0.5469519 object centre (A): 47.91050 151.7390 28.98000 number of atom coordinates read : 4568 total number of charged atoms : 4386 net assigned charge : 2.906039 assigned positive charge : 701.1468 centred at (gu) : 91.70362 89.26423 87.25431 assigned negative charge : -698.2442 centred at (gu) : 91.66557 89.17749 87.26628 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 8727 nv = 96 ne = 84 npr = 91908 no. pairs analyzed = 91908 no. exposed pairs = 5453 no. arc points = 37918 no. surface atoms = 1842 nbur = 2726 mkacc time = 0.2000000 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 = 1.568000 m= 400 mr = 4724 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3927 ## 536 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 11670 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1148542E-10 3.0231945E-11 midg,1,midg; midg,igrid,midg -9.0989405E-10 9.1398711E-10 1,midg,midg; igrid,midg,midg -1.4571164E-10 8.9694446E-10 gauss-seidel spectral radius is 0.9828822 estimated iterations to convergence 63 setup time was (sec) 0.7200000 now iterating at: 16:43:49 rms-change max change #iterations 9.3948722E-02 14.61030 at 10iterations 6.5482715E-03 0.9575424 at 20iterations 5.9895404E-04 8.4941864E-02 at 30iterations 1.3339095E-04 1.8543243E-02 at 40iterations 4.0663908E-05 6.0839653E-03 at 50iterations finished qdiffx linear iterations at : 16:43:52 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 4.0663908E-05 6.0839653E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 16:43:53 4.311u 0.236s 0:04.84 93.8% 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 16:43:53 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4568 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 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: 1.640856 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): 16.92800 78.89300 ymin,ymax (A): 119.1950 184.2830 zmin,zma (A): -1.737000 59.69700 x,y,z range (A): 61.96500 65.08799 61.43400 scale (grids/A): 1.640856 object centre (A): 47.91050 151.7390 28.98000 number of atom coordinates read : 4568 total number of charged atoms : 4386 net assigned charge : 2.906039 assigned positive charge : 701.1468 centred at (gu) : 95.10969 87.79112 81.76189 assigned negative charge : -698.2442 centred at (gu) : 94.99670 87.53221 81.79872 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 98371 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37918 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30858 mr = 69023 m= 3484 mr = 21454 m= 110 mr = 1951 m= 0 mr = 19 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 0.7000000 number of dielectric boundary points 40376 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 489 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 33629 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) : 0.5469519 object centre at (A) : 47.91050 151.7390 28.98000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5849740E-03 8.6510861E-03 midg,1,midg; midg,igrid,midg 1.4618027E-02 3.3609290E-02 1,midg,midg; igrid,midg,midg -1.0763876E-02 -1.5668720E-02 gauss-seidel spectral radius is 0.9983528 estimated iterations to convergence 196 setup time was (sec) 1.030000 now iterating at: 16:43:54 rms-change max change #iterations 4.373569 203.9157 at 10iterations 1.897990 92.69911 at 20iterations 0.8221024 30.97477 at 30iterations 0.3581927 11.68585 at 40iterations 0.1561482 5.136588 at 50iterations 6.7920789E-02 2.161331 at 60iterations 2.9539019E-02 0.9571075 at 70iterations 1.2884957E-02 0.3752499 at 80iterations 5.6318133E-03 0.1784573 at 90iterations 2.4630555E-03 7.5592041E-02 at 100iterations 1.0877419E-03 3.1902313E-02 at 110iterations 4.8140570E-04 1.4974594E-02 at 120iterations finished qdiffx linear iterations at : 16:44:03 total time elapsed so far: 9.750000 # loops : 120 mean,max change (kT/e) : 4.8140570E-04 1.4974594E-02 energy calculations done at 9.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.920000 DelPhi exited at 16:44:04 9.923u 0.274s 0:10.58 96.3% 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 16:44:04 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: 364 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4568 !!! WARNING: GLM 204 has a net charge of -0.0940 !!! WARNING: FAD 994 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: 2.461284 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): 16.92800 78.89300 ymin,ymax (A): 119.1950 184.2830 zmin,zma (A): -1.737000 59.69700 x,y,z range (A): 61.96500 65.08799 61.43400 scale (grids/A): 2.461284 object centre (A): 47.91050 151.7390 28.98000 number of atom coordinates read : 4568 total number of charged atoms : 4386 net assigned charge : 2.906039 assigned positive charge : 701.1468 centred at (gu) : 97.66438 86.68668 77.64252 assigned negative charge : -698.2442 centred at (gu) : 97.49484 86.29841 77.69790 start vw surface at 0.1800000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 229248 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37918 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 106599 mr = 168864 m= 31249 mr = 85319 m= 5808 mr = 23756 m= 507 mr = 4125 m= 6 mr = 286 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 803 time to turn everything in is 1.770000 number of dielectric boundary points 91067 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 35054 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) : 1.640856 object centre at (A) : 47.91050 151.7390 28.98000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9320585E-04 0.1818561 midg,1,midg; midg,igrid,midg 0.2198016 0.6027073 1,midg,midg; igrid,midg,midg -0.1433155 -0.2597639 gauss-seidel spectral radius is 0.9992180 estimated iterations to convergence 282 setup time was (sec) 2.120000 now iterating at: 16:44:06 rms-change max change #iterations 11.16737 340.5575 at 10iterations 6.457226 133.7940 at 20iterations 3.704633 71.37017 at 30iterations 2.125147 40.19347 at 40iterations 1.212170 25.49901 at 50iterations 0.6910123 12.07328 at 60iterations 0.3929599 6.742065 at 70iterations 0.2229225 4.149231 at 80iterations 0.1266647 2.075951 at 90iterations 7.1723841E-02 1.134396 at 100iterations 4.0608343E-02 0.6632576 at 110iterations 2.3050442E-02 0.4371624 at 120iterations 1.3052636E-02 0.2511215 at 130iterations 7.3847803E-03 0.1252145 at 140iterations 4.1822898E-03 6.7033768E-02 at 150iterations 2.3689389E-03 3.8739204E-02 at 160iterations 1.3386062E-03 2.2171021E-02 at 170iterations 7.5843529E-04 1.3686180E-02 at 180iterations finished qdiffx linear iterations at : 16:44:20 total time elapsed so far: 16.34000 # loops : 180 mean,max change (kT/e) : 7.5843529E-04 1.3686180E-02 energy calculations done at 16.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.51000 DelPhi exited at 16:44:21 16.515u 0.303s 0:17.13 98.1% 0+0k 0+0io 0pf+0w