Mon Oct 10 23:15:41 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 Mon Oct 10 2011 at 23:15:41 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4117 !!! WARNING: GLM 542 has a net charge of -0.0940 !!! WARNING: GLM 546 has a net charge of -0.0940 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: 0.4959944 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): -18.56000 47.12900 ymin,ymax (A): -19.12700 42.99700 zmin,zma (A): 5.002000 76.77700 x,y,z range (A): 65.68900 62.12400 71.77500 scale (grids/A): 0.4959944 object centre (A): 14.28450 11.93500 40.88950 number of atom coordinates read : 4117 total number of charged atoms : 3951 net assigned charge : 3.812024 assigned positive charge : 621.7097 centred at (gu) : 90.62915 87.85835 92.86819 assigned negative charge : -617.9009 centred at (gu) : 90.68105 87.75033 92.82064 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6362 nv = 96 ne = 84 npr = 81485 no. pairs analyzed = 81485 no. exposed pairs = 5260 no. arc points = 37167 no. surface atoms = 1750 nbur = 2367 mkacc time = 0.1400000 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 = 1.708000 m= 204 mr = 3204 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2700000 number of dielectric boundary points 3362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3458 ## 583 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 8560 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1786743E-11 1.8428142E-10 midg,1,midg; midg,igrid,midg -1.7918936E-10 8.5495735E-11 1,midg,midg; igrid,midg,midg 7.4716774E-11 -3.7818585E-11 gauss-seidel spectral radius is 0.9791741 estimated iterations to convergence 57 setup time was (sec) 0.4600000 now iterating at: 23:15:42 rms-change max change #iterations 5.5589419E-02 9.776373 at 10iterations 3.3434259E-03 0.6063080 at 20iterations 3.0854798E-04 4.3281555E-02 at 30iterations 5.7133806E-05 7.2469711E-03 at 40iterations 1.2839715E-05 1.6641617E-03 at 50iterations finished qdiffx linear iterations at : 23:15:44 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.2839715E-05 1.6641617E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 23:15:45 3.451u 0.168s 0:04.09 88.2% 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 Mon Oct 10 2011 at 23:15:45 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4117 !!! WARNING: GLM 542 has a net charge of -0.0940 !!! WARNING: GLM 546 has a net charge of -0.0940 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: 1.487983 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): -18.56000 47.12900 ymin,ymax (A): -19.12700 42.99700 zmin,zma (A): 5.002000 76.77700 x,y,z range (A): 65.68900 62.12400 71.77500 scale (grids/A): 1.487983 object centre (A): 14.28450 11.93500 40.88950 number of atom coordinates read : 4117 total number of charged atoms : 3951 net assigned charge : 3.812024 assigned positive charge : 621.7097 centred at (gu) : 91.88610 83.57418 98.60321 assigned negative charge : -617.9009 centred at (gu) : 92.04295 83.25063 98.46154 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72486 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37167 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 20216 mr = 48473 m= 1556 mr = 13460 m= 26 mr = 675 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 2423 time to turn everything in is 0.3500000 number of dielectric boundary points 31676 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 465 ## 14 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 29328 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) : 0.4959944 object centre at (A) : 14.28450 11.93500 40.88950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6468594E-03 2.5547052E-02 midg,1,midg; midg,igrid,midg -1.0669205E-02 3.4761615E-03 1,midg,midg; igrid,midg,midg 8.7100649E-03 -3.2008779E-03 gauss-seidel spectral radius is 0.9978821 estimated iterations to convergence 173 setup time was (sec) 0.5600000 now iterating at: 23:15:46 rms-change max change #iterations 3.232245 143.2986 at 10iterations 1.256930 41.45630 at 20iterations 0.4889170 17.59811 at 30iterations 0.1906440 9.189063 at 40iterations 7.4308410E-02 2.482376 at 50iterations 2.8972425E-02 1.034916 at 60iterations 1.1319355E-02 0.4134464 at 70iterations 4.4302777E-03 0.1754246 at 80iterations 1.7462306E-03 6.3152313E-02 at 90iterations 6.9709518E-04 2.4276733E-02 at 100iterations 2.8366345E-04 1.0608673E-02 at 110iterations 1.2121095E-04 4.2705536E-03 at 120iterations finished qdiffx linear iterations at : 23:15:53 total time elapsed so far: 7.500000 # loops : 120 mean,max change (kT/e) : 1.2121095E-04 4.2705536E-03 energy calculations done at 7.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.630000 DelPhi exited at 23:15:53 7.630u 0.205s 0:08.11 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 Mon Oct 10 2011 at 23:15:53 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4117 !!! WARNING: GLM 542 has a net charge of -0.0940 !!! WARNING: GLM 546 has a net charge of -0.0940 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: 2.231975 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): -18.56000 47.12900 ymin,ymax (A): -19.12700 42.99700 zmin,zma (A): 5.002000 76.77700 x,y,z range (A): 65.68900 62.12400 71.77500 scale (grids/A): 2.231975 object centre (A): 14.28450 11.93500 40.88950 number of atom coordinates read : 4117 total number of charged atoms : 3951 net assigned charge : 3.812024 assigned positive charge : 621.7097 centred at (gu) : 92.82877 80.36078 102.9046 assigned negative charge : -617.9009 centred at (gu) : 93.06442 79.87592 102.6924 start vw surface at 0.1100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 169097 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37167 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 72847 mr = 119598 m= 17957 mr = 56533 m= 2138 mr = 13178 m= 55 mr = 1244 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 7901 time to turn everything in is 0.8400000 number of dielectric boundary points 71532 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 73 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 31478 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) : 1.487983 object centre at (A) : 14.28450 11.93500 40.88950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6251956E-02 0.5068316 midg,1,midg; midg,igrid,midg -0.2222925 5.0244112E-02 1,midg,midg; igrid,midg,midg 0.1334273 -2.6492203E-02 gauss-seidel spectral radius is 0.9990476 estimated iterations to convergence 256 setup time was (sec) 1.070000 now iterating at: 23:15:55 rms-change max change #iterations 8.935118 360.9710 at 10iterations 4.930493 117.3657 at 20iterations 2.693609 68.85031 at 30iterations 1.463019 33.37627 at 40iterations 0.7914972 18.42479 at 50iterations 0.4268477 10.56776 at 60iterations 0.2294237 5.259809 at 70iterations 0.1233653 2.629016 at 80iterations 6.6282086E-02 1.500542 at 90iterations 3.5496868E-02 0.8428073 at 100iterations 1.9020982E-02 0.4728789 at 110iterations 1.0176132E-02 0.2293108 at 120iterations 5.4567140E-03 0.1190796 at 130iterations 2.9152685E-03 7.2196960E-02 at 140iterations 1.5577007E-03 3.2890320E-02 at 150iterations 8.3483465E-04 1.6954899E-02 at 160iterations 4.4649365E-04 9.6588135E-03 at 170iterations 2.3983295E-04 5.4626465E-03 at 180iterations finished qdiffx linear iterations at : 23:16:06 total time elapsed so far: 12.14000 # loops : 180 mean,max change (kT/e) : 2.3983295E-04 5.4626465E-03 energy calculations done at 12.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.27000 DelPhi exited at 23:16:06 12.276u 0.208s 0:12.80 97.4% 0+0k 0+0io 0pf+0w