Sun Oct 9 06:15:53 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 Sun Oct 9 2011 at 06:15:53 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6636344 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): 1.792000 44.37600 ymin,ymax (A): -9.402000 39.11600 zmin,zma (A): -24.34100 29.30300 x,y,z range (A): 42.58400 48.51800 53.64400 scale (grids/A): 0.6636344 object centre (A): 23.08400 14.85700 2.481000 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -1.499986 assigned positive charge : 299.6400 centred at (gu) : 90.03714 88.94473 88.22847 assigned negative charge : -301.1401 centred at (gu) : 89.87000 88.78394 88.20119 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5920 nv = 96 ne = 84 npr = 41782 no. pairs analyzed = 41782 no. exposed pairs = 2443 no. arc points = 17571 no. surface atoms = 822 nbur = 1172 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 3281 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 49 time to turn everything in is 0.2500000 number of dielectric boundary points 2959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1690 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6872 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2022704E-08 5.0681842E-10 midg,1,midg; midg,igrid,midg -3.8931478E-08 1.8198913E-08 1,midg,midg; igrid,midg,midg -3.2000070E-08 2.3975932E-08 gauss-seidel spectral radius is 0.9881759 estimated iterations to convergence 75 setup time was (sec) 0.4800000 now iterating at: 06:15:54 rms-change max change #iterations 0.1519344 23.48866 at 10iterations 1.6574565E-02 2.510248 at 20iterations 1.7527714E-03 0.2936025 at 30iterations 1.8630597E-04 3.1723976E-02 at 40iterations 1.9937695E-05 3.0126572E-03 at 50iterations finished qdiffx linear iterations at : 06:15:56 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.9937695E-05 3.0126572E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 06:15:57 3.332u 0.198s 0:03.79 92.8% 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 Sun Oct 9 2011 at 06:15:57 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.990903 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): 1.792000 44.37600 ymin,ymax (A): -9.402000 39.11600 zmin,zma (A): -24.34100 29.30300 x,y,z range (A): 42.58400 48.51800 53.64400 scale (grids/A): 1.990903 object centre (A): 23.08400 14.85700 2.481000 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -1.499986 assigned positive charge : 299.6400 centred at (gu) : 90.11136 86.83427 84.68531 assigned negative charge : -301.1401 centred at (gu) : 89.61005 86.35205 84.60398 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63174 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17571 grid for indexing accessible points = 1.400000 m= 23411 mr = 43378 m= 4102 mr = 17575 m= 310 mr = 2787 m= 2 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1669 time to turn everything in is 0.4700000 number of dielectric boundary points 27121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14666 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) : 0.6636344 object centre at (A) : 23.08400 14.85700 2.481000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9705787E-02 1.8084688E-02 midg,1,midg; midg,igrid,midg -3.1443454E-02 1.0913218E-02 1,midg,midg; igrid,midg,midg -2.6480732E-02 1.6471583E-02 gauss-seidel spectral radius is 0.9986818 estimated iterations to convergence 218 setup time was (sec) 0.7600000 now iterating at: 06:15:58 rms-change max change #iterations 4.076358 212.2661 at 10iterations 1.925914 67.18382 at 20iterations 0.9125984 33.24427 at 30iterations 0.4336453 15.62591 at 40iterations 0.2050229 6.936732 at 50iterations 9.7528242E-02 3.483719 at 60iterations 4.6211828E-02 1.579458 at 70iterations 2.1907896E-02 0.8231840 at 80iterations 1.0413319E-02 0.3533897 at 90iterations 4.9234219E-03 0.1706133 at 100iterations 2.3349337E-03 7.3986053E-02 at 110iterations 1.1065145E-03 3.6061764E-02 at 120iterations finished qdiffx linear iterations at : 06:16:05 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 1.1065145E-03 3.6061764E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.550000 DelPhi exited at 06:16:05 7.552u 0.243s 0:08.06 96.6% 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 06:16:05 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1994 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NAP 187 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.986355 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): 1.792000 44.37600 ymin,ymax (A): -9.402000 39.11600 zmin,zma (A): -24.34100 29.30300 x,y,z range (A): 42.58400 48.51800 53.64400 scale (grids/A): 2.986355 object centre (A): 23.08400 14.85700 2.481000 number of atom coordinates read : 1994 total number of charged atoms : 1855 net assigned charge : -1.499986 assigned positive charge : 299.6400 centred at (gu) : 90.16712 85.25135 82.02797 assigned negative charge : -301.1401 centred at (gu) : 89.41512 84.52806 81.90595 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 145516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17571 grid for indexing accessible points = 1.400000 m= 74938 mr = 104657 m= 28586 mr = 61838 m= 7814 mr = 23504 m= 1392 mr = 6178 m= 107 mr = 1008 m= 3 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 5549 time to turn everything in is 1.170000 number of dielectric boundary points 61137 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 14840 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) : 1.990903 object centre at (A) : 23.08400 14.85700 2.481000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5331710 0.3662219 midg,1,midg; midg,igrid,midg -0.2203824 0.1437606 1,midg,midg; igrid,midg,midg -0.2564585 0.1351030 gauss-seidel spectral radius is 0.9992548 estimated iterations to convergence 289 setup time was (sec) 1.470000 now iterating at: 06:16:07 rms-change max change #iterations 9.331439 342.3677 at 10iterations 5.359498 133.4832 at 20iterations 3.091418 61.32198 at 30iterations 1.775371 39.33098 at 40iterations 1.020534 21.44345 at 50iterations 0.5853173 11.37079 at 60iterations 0.3354047 6.497533 at 70iterations 0.1918531 3.742222 at 80iterations 0.1099443 2.093872 at 90iterations 6.3051380E-02 1.187600 at 100iterations 3.6052480E-02 0.7186902 at 110iterations 2.0630701E-02 0.3847198 at 120iterations 1.1803933E-02 0.2301559 at 130iterations 6.7608273E-03 0.1309500 at 140iterations 3.8727317E-03 7.7419281E-02 at 150iterations 2.2228609E-03 4.3074608E-02 at 160iterations 1.2717906E-03 2.5752544E-02 at 170iterations 7.2751363E-04 1.3703346E-02 at 180iterations finished qdiffx linear iterations at : 06:16:17 total time elapsed so far: 12.04000 # loops : 180 mean,max change (kT/e) : 7.2751363E-04 1.3703346E-02 energy calculations done at 12.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.21000 DelPhi exited at 06:16:18 12.214u 0.253s 0:12.72 97.9% 0+0k 0+0io 0pf+0w