Sat Oct 15 15:26:51 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+sph.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 = amb.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 15 2011 at 15:26:51 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2743 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6641915 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): -12.35400 37.01600 ymin,ymax (A): -25.88500 22.44400 zmin,zma (A): -8.235000 45.36400 x,y,z range (A): 49.37000 48.32900 53.59900 scale (grids/A): 0.6641915 object centre (A): 12.33100 -1.720500 18.56450 number of atom coordinates read : 2743 total number of charged atoms : 2591 net assigned charge : 2.162012 assigned positive charge : 413.4357 centred at (gu) : 90.31975 90.39148 91.30949 assigned negative charge : -411.2744 centred at (gu) : 90.06380 90.21428 91.21880 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8063 nv = 96 ne = 84 npr = 56404 no. pairs analyzed = 56404 no. exposed pairs = 3316 no. arc points = 22812 no. surface atoms = 1111 nbur = 1632 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 458 mr = 4627 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.2000000 number of dielectric boundary points 3837 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2283 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1906941E-08 3.4894349E-08 midg,1,midg; midg,igrid,midg -3.3583976E-08 5.0048826E-08 1,midg,midg; igrid,midg,midg -5.2053991E-08 6.8052451E-08 gauss-seidel spectral radius is 0.9882587 estimated iterations to convergence 75 setup time was (sec) 0.4100000 now iterating at: 15:26:52 rms-change max change #iterations 0.1727081 23.28956 at 10iterations 1.9344542E-02 2.529808 at 20iterations 2.1905499E-03 0.3653812 at 30iterations 3.0386171E-04 4.6886444E-02 at 40iterations 6.6555418E-05 8.4915161E-03 at 50iterations finished qdiffx linear iterations at : 15:26:57 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 6.6555418E-05 8.4915161E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 15:26:58 3.532u 0.196s 0:06.91 53.8% 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 15 2011 at 15:26:58 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2743 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.992574 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): -12.35400 37.01600 ymin,ymax (A): -25.88500 22.44400 zmin,zma (A): -8.235000 45.36400 x,y,z range (A): 49.37000 48.32900 53.59900 scale (grids/A): 1.992574 object centre (A): 12.33100 -1.720500 18.56450 number of atom coordinates read : 2743 total number of charged atoms : 2591 net assigned charge : 2.162012 assigned positive charge : 413.4357 centred at (gu) : 90.95893 91.17418 93.92792 assigned negative charge : -411.2744 centred at (gu) : 90.19141 90.64245 93.65623 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 86522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22812 grid for indexing accessible points = 1.400000 m= 32931 mr = 61484 m= 5494 mr = 24877 m= 366 mr = 3530 m= 5 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1276 time to turn everything in is 0.4400000 number of dielectric boundary points 35262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20503 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) : 0.6641915 object centre at (A) : 12.33100 -1.720500 18.56450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1788294E-02 3.4841748E-03 midg,1,midg; midg,igrid,midg -1.3814930E-02 3.6838591E-02 1,midg,midg; igrid,midg,midg -9.9664405E-03 8.3840244E-02 gauss-seidel spectral radius is 0.9987592 estimated iterations to convergence 225 setup time was (sec) 0.6600000 now iterating at: 15:26:59 rms-change max change #iterations 4.778035 221.2085 at 10iterations 2.325678 79.56752 at 20iterations 1.126081 42.13586 at 30iterations 0.5477100 16.61301 at 40iterations 0.2675653 7.930908 at 50iterations 0.1298539 3.761284 at 60iterations 6.3074119E-02 2.036610 at 70iterations 3.0735521E-02 0.8725691 at 80iterations 1.5003172E-02 0.4628239 at 90iterations 7.3003229E-03 0.2037425 at 100iterations 3.5894539E-03 9.8077774E-02 at 110iterations 1.7663921E-03 5.4927826E-02 at 120iterations finished qdiffx linear iterations at : 15:27:07 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 1.7663921E-03 5.4927826E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.390000 DelPhi exited at 15:27:07 8.390u 0.232s 0:09.03 95.4% 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 Sat Oct 15 2011 at 15:27:07 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2743 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.988862 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): -12.35400 37.01600 ymin,ymax (A): -25.88500 22.44400 zmin,zma (A): -8.235000 45.36400 x,y,z range (A): 49.37000 48.32900 53.59900 scale (grids/A): 2.988862 object centre (A): 12.33100 -1.720500 18.56450 number of atom coordinates read : 2743 total number of charged atoms : 2591 net assigned charge : 2.162012 assigned positive charge : 413.4357 centred at (gu) : 91.43806 91.76125 95.89175 assigned negative charge : -411.2744 centred at (gu) : 90.28705 90.96355 95.48431 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 200023 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22812 grid for indexing accessible points = 1.400000 m= 105292 mr = 148600 m= 39810 mr = 87384 m= 10013 mr = 32608 m= 1474 mr = 7554 m= 134 mr = 998 m= 4 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 4536 time to turn everything in is 1.130000 number of dielectric boundary points 79520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 20718 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) : 1.992574 object centre at (A) : 12.33100 -1.720500 18.56450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6490039 0.2227432 midg,1,midg; midg,igrid,midg -0.1448720 0.4207113 1,midg,midg; igrid,midg,midg -7.9724416E-02 0.7211144 gauss-seidel spectral radius is 0.9992887 estimated iterations to convergence 296 setup time was (sec) 1.390000 now iterating at: 15:27:09 rms-change max change #iterations 10.95334 426.1088 at 10iterations 6.443877 144.8414 at 20iterations 3.789603 74.24245 at 30iterations 2.228992 46.46049 at 40iterations 1.306929 28.82387 at 50iterations 0.7648236 15.82579 at 60iterations 0.4478360 7.802582 at 70iterations 0.2615627 4.740927 at 80iterations 0.1529803 2.613073 at 90iterations 8.8981964E-02 1.443418 at 100iterations 5.1999524E-02 0.9297028 at 110iterations 3.0351823E-02 0.5248260 at 120iterations 1.7739505E-02 0.2954941 at 130iterations 1.0366252E-02 0.1745920 at 140iterations 6.0833655E-03 0.1139183 at 150iterations 3.6017939E-03 6.4134121E-02 at 160iterations 2.1558774E-03 3.7296295E-02 at 170iterations 1.3146645E-03 2.3736954E-02 at 180iterations finished qdiffx linear iterations at : 15:27:28 total time elapsed so far: 13.51000 # loops : 180 mean,max change (kT/e) : 1.3146645E-03 2.3736954E-02 energy calculations done at 13.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.65000 DelPhi exited at 15:27:29 13.648u 0.250s 0:21.55 64.4% 0+0k 0+0io 0pf+0w