Sun Oct 9 06:09:37 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 06:09:37 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1987 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6849842 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): 1.896000 44.28200 ymin,ymax (A): -9.192000 37.42300 zmin,zma (A): -24.35900 27.61300 x,y,z range (A): 42.38600 46.61500 51.97200 scale (grids/A): 0.6849842 object centre (A): 23.08900 14.11550 1.627000 number of atom coordinates read : 1987 total number of charged atoms : 1844 net assigned charge : -2.593985 assigned positive charge : 299.7130 centred at (gu) : 89.97277 89.27549 88.78921 assigned negative charge : -302.3071 centred at (gu) : 89.82771 89.10976 88.74806 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6282 nv = 96 ne = 84 npr = 41663 no. pairs analyzed = 41663 no. exposed pairs = 2448 no. arc points = 17558 no. surface atoms = 823 nbur = 1164 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 405 mr = 3463 m= 3 mr = 75 m= 0 mr = 0 time to grow re-entrant surface = 7.0000008E-02 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.1600000 number of dielectric boundary points 3152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1594 ## 131 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 7055 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0314272E-08 -3.9087503E-10 midg,1,midg; midg,igrid,midg -6.9611545E-08 2.9606635E-08 1,midg,midg; igrid,midg,midg -5.4258290E-08 2.8569650E-08 gauss-seidel spectral radius is 0.9888936 estimated iterations to convergence 77 setup time was (sec) 0.3500000 now iterating at: 06:09:37 rms-change max change #iterations 0.1780412 26.86593 at 10iterations 2.0226467E-02 2.892171 at 20iterations 2.3265397E-03 0.3201599 at 30iterations 2.6547979E-04 3.6060333E-02 at 40iterations 3.0320372E-05 4.6920776E-03 at 50iterations finished qdiffx linear iterations at : 06:09:40 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 3.0320372E-05 4.6920776E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 06:09:41 3.367u 0.179s 0:03.81 92.6% 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 06:09:41 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1987 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.054953 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): 1.896000 44.28200 ymin,ymax (A): -9.192000 37.42300 zmin,zma (A): -24.35900 27.61300 x,y,z range (A): 42.38600 46.61500 51.97200 scale (grids/A): 2.054953 object centre (A): 23.08900 14.11550 1.627000 number of atom coordinates read : 1987 total number of charged atoms : 1844 net assigned charge : -2.593985 assigned positive charge : 299.7130 centred at (gu) : 89.91808 87.82646 86.36766 assigned negative charge : -302.3071 centred at (gu) : 89.48306 87.32942 86.24416 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66900 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17558 grid for indexing accessible points = 1.400000 m= 25805 mr = 45933 m= 4855 mr = 19553 m= 427 mr = 3369 m= 6 mr = 206 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 2596 time to turn everything in is 0.3500000 number of dielectric boundary points 28932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 14609 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) : 0.6849842 object centre at (A) : 23.08900 14.11550 1.627000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2390147E-02 2.7624855E-02 midg,1,midg; midg,igrid,midg -4.1280307E-02 1.3849877E-02 1,midg,midg; igrid,midg,midg -3.5178624E-02 2.4603564E-02 gauss-seidel spectral radius is 0.9987576 estimated iterations to convergence 225 setup time was (sec) 0.5500000 now iterating at: 06:09:42 rms-change max change #iterations 4.358255 250.3457 at 10iterations 2.090725 94.37763 at 20iterations 1.014595 34.97614 at 30iterations 0.4920560 16.02896 at 40iterations 0.2375779 7.689781 at 50iterations 0.1156504 3.921774 at 60iterations 5.5998906E-02 1.857184 at 70iterations 2.7116127E-02 0.8921204 at 80iterations 1.3070883E-02 0.4327927 at 90iterations 6.3854889E-03 0.2555466 at 100iterations 3.0759794E-03 9.9959373E-02 at 110iterations 1.4970461E-03 4.4494629E-02 at 120iterations finished qdiffx linear iterations at : 06:09:49 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.4970461E-03 4.4494629E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 06:09:49 7.772u 0.208s 0:08.26 96.4% 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 06:09:49 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1987 !!! WARNING: GLM 35 has a net charge of -0.0940 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.082429 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): 1.896000 44.28200 ymin,ymax (A): -9.192000 37.42300 zmin,zma (A): -24.35900 27.61300 x,y,z range (A): 42.38600 46.61500 51.97200 scale (grids/A): 3.082429 object centre (A): 23.08900 14.11550 1.627000 number of atom coordinates read : 1987 total number of charged atoms : 1844 net assigned charge : -2.593985 assigned positive charge : 299.7130 centred at (gu) : 89.87727 86.73978 84.55160 assigned negative charge : -302.3071 centred at (gu) : 89.22456 85.99422 84.36623 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 154473 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17558 grid for indexing accessible points = 1.400000 m= 81082 mr = 110994 m= 31992 mr = 67220 m= 9058 mr = 26430 m= 1828 mr = 7264 m= 138 mr = 1348 m= 3 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 8491 time to turn everything in is 1.020000 number of dielectric boundary points 65259 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 14752 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) : 2.054953 object centre at (A) : 23.08900 14.11550 1.627000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5665416 0.8602588 midg,1,midg; midg,igrid,midg -0.3386478 0.1554717 1,midg,midg; igrid,midg,midg -0.3014292 0.2163505 gauss-seidel spectral radius is 0.9992750 estimated iterations to convergence 293 setup time was (sec) 1.250000 now iterating at: 06:09:51 rms-change max change #iterations 9.751114 459.9745 at 10iterations 5.635238 113.6689 at 20iterations 3.255342 71.44295 at 30iterations 1.882722 35.48481 at 40iterations 1.086711 21.41549 at 50iterations 0.6285864 11.95681 at 60iterations 0.3627612 6.763619 at 70iterations 0.2091598 4.369732 at 80iterations 0.1206496 2.368711 at 90iterations 6.9657318E-02 1.391227 at 100iterations 4.0129323E-02 0.8377075 at 110iterations 2.3147928E-02 0.4883690 at 120iterations 1.3351587E-02 0.2434616 at 130iterations 7.7136206E-03 0.1413794 at 140iterations 4.4513340E-03 8.2912445E-02 at 150iterations 2.5583492E-03 4.6966791E-02 at 160iterations 1.4796624E-03 2.6512146E-02 at 170iterations 8.5247116E-04 1.5075684E-02 at 180iterations finished qdiffx linear iterations at : 06:10:02 total time elapsed so far: 12.53000 # loops : 180 mean,max change (kT/e) : 8.5247116E-04 1.5075684E-02 energy calculations done at 12.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 06:10:02 12.662u 0.223s 0:13.15 97.9% 0+0k 0+0io 0pf+0w