Mon Oct 10 17:08:31 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 Mon Oct 10 2011 at 17:08:31 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4295 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5111932 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): -15.91300 36.49600 ymin,ymax (A): -32.13100 31.23000 zmin,zma (A): -3.978000 65.66300 x,y,z range (A): 52.40900 63.36100 69.64100 scale (grids/A): 0.5111932 object centre (A): 10.29150 -0.4505005 30.84250 number of atom coordinates read : 4295 total number of charged atoms : 4051 net assigned charge : 4.700032 assigned positive charge : 638.8283 centred at (gu) : 90.23869 90.75201 87.62564 assigned negative charge : -634.1321 centred at (gu) : 90.11334 90.80454 87.64725 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 7084 nv = 96 ne = 84 npr = 87436 no. pairs analyzed = 87436 no. exposed pairs = 5514 no. arc points = 38128 no. surface atoms = 1845 nbur = 2450 mkacc time = 0.3000000 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 = 1.652000 m= 250 mr = 3596 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.3399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 3728 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3649 ## 540 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 9424 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2017460E-10 9.6961588E-12 midg,1,midg; midg,igrid,midg 1.5545458E-10 -7.0434748E-11 1,midg,midg; igrid,midg,midg -2.1717034E-10 3.7916920E-10 gauss-seidel spectral radius is 0.9803951 estimated iterations to convergence 59 setup time was (sec) 0.9900000 now iterating at: 17:08:32 rms-change max change #iterations 6.5749340E-02 10.99687 at 10iterations 3.9695348E-03 0.7945824 at 20iterations 4.4549268E-04 6.0146838E-02 at 30iterations 1.3649400E-04 1.9118737E-02 at 40iterations 4.9806153E-05 7.4372292E-03 at 50iterations finished qdiffx linear iterations at : 17:08:39 total time elapsed so far: 7.630000 # loops : 50 mean,max change (kT/e) : 4.9806153E-05 7.4372292E-03 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 17:08:39 7.880u 0.407s 0:08.63 95.9% 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 17:08:39 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4295 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.533579 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): -15.91300 36.49600 ymin,ymax (A): -32.13100 31.23000 zmin,zma (A): -3.978000 65.66300 x,y,z range (A): 52.40900 63.36100 69.64100 scale (grids/A): 1.533579 object centre (A): 10.29150 -0.4505005 30.84250 number of atom coordinates read : 4295 total number of charged atoms : 4051 net assigned charge : 4.700032 assigned positive charge : 638.8283 centred at (gu) : 90.71505 92.25464 82.87537 assigned negative charge : -634.1321 centred at (gu) : 90.33986 92.41329 82.94150 start vw surface at 0.2200000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 79797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38128 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 22689 mr = 54262 m= 1952 mr = 14802 m= 30 mr = 796 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 0.8300000 number of dielectric boundary points 34608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 436 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 30417 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) : 0.5111932 object centre at (A) : 10.29150 -0.4505005 30.84250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1934826E-03 8.7952316E-03 midg,1,midg; midg,igrid,midg -6.3955010E-04 -9.8640863E-03 1,midg,midg; igrid,midg,midg -2.9941923E-03 9.1051329E-03 gauss-seidel spectral radius is 0.9980695 estimated iterations to convergence 181 setup time was (sec) 1.160000 now iterating at: 17:08:41 rms-change max change #iterations 3.538556 189.0519 at 10iterations 1.428998 50.08037 at 20iterations 0.5800831 19.12386 at 30iterations 0.2353026 8.046074 at 40iterations 9.5161170E-02 3.125605 at 50iterations 3.8915455E-02 1.354168 at 60iterations 1.5779305E-02 0.5825043 at 70iterations 6.4489865E-03 0.2377625 at 80iterations 2.6454420E-03 8.3251953E-02 at 90iterations 1.1098735E-03 3.5711288E-02 at 100iterations 4.8498751E-04 1.8760681E-02 at 110iterations 2.3171587E-04 8.5735321E-03 at 120iterations finished qdiffx linear iterations at : 17:08:50 total time elapsed so far: 10.23000 # loops : 120 mean,max change (kT/e) : 2.3171587E-04 8.5735321E-03 energy calculations done at 10.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.43000 DelPhi exited at 17:08:51 10.436u 0.485s 0:11.19 97.4% 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 Mon Oct 10 2011 at 17:08:51 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4295 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: ZN8 820 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.300369 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): -15.91300 36.49600 ymin,ymax (A): -32.13100 31.23000 zmin,zma (A): -3.978000 65.66300 x,y,z range (A): 52.40900 63.36100 69.64100 scale (grids/A): 2.300369 object centre (A): 10.29150 -0.4505005 30.84250 number of atom coordinates read : 4295 total number of charged atoms : 4051 net assigned charge : 4.700032 assigned positive charge : 638.8283 centred at (gu) : 91.07207 93.38167 79.31271 assigned negative charge : -634.1321 centred at (gu) : 90.50967 93.61993 79.41208 start vw surface at 0.2200000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 186376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38128 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 81540 mr = 133772 m= 20092 mr = 63201 m= 2910 mr = 14287 m= 140 mr = 1695 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 177 time to turn everything in is 2.020000 number of dielectric boundary points 78060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 2.210000 number of grid points assigned charge 32336 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) : 1.533579 object centre at (A) : 10.29150 -0.4505005 30.84250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1615360 0.2479421 midg,1,midg; midg,igrid,midg -7.8749709E-02 -0.2397203 1,midg,midg; igrid,midg,midg -3.8422588E-02 0.1258582 gauss-seidel spectral radius is 0.9991392 estimated iterations to convergence 269 setup time was (sec) 2.420000 now iterating at: 17:08:53 rms-change max change #iterations 9.623039 275.7200 at 10iterations 5.455406 118.5388 at 20iterations 3.074819 63.54911 at 30iterations 1.724715 40.15034 at 40iterations 0.9662761 24.38769 at 50iterations 0.5382080 10.93773 at 60iterations 0.2992451 6.688527 at 70iterations 0.1657298 3.341388 at 80iterations 9.1991700E-02 2.046382 at 90iterations 5.0854858E-02 1.021126 at 100iterations 2.8141180E-02 0.5701461 at 110iterations 1.5530394E-02 0.3169556 at 120iterations 8.5888347E-03 0.1911159 at 130iterations 4.7444040E-03 9.7908020E-02 at 140iterations 2.6218379E-03 6.1645508E-02 at 150iterations 1.4533021E-03 2.7828991E-02 at 160iterations 8.0550538E-04 1.7250061E-02 at 170iterations 4.5086205E-04 9.3197823E-03 at 180iterations finished qdiffx linear iterations at : 17:09:09 total time elapsed so far: 17.62000 # loops : 180 mean,max change (kT/e) : 4.5086205E-04 9.3197823E-03 energy calculations done at 17.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.85000 DelPhi exited at 17:09:10 17.859u 0.476s 0:19.13 95.7% 0+0k 0+0io 0pf+0w