Mon Oct 10 16:02:39 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 16:02:39 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4760 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN9 975 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5394920 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): -19.99500 45.99300 ymin,ymax (A): 8.247999 72.14600 zmin,zma (A): 33.89900 94.86400 x,y,z range (A): 65.98800 63.89800 60.96500 scale (grids/A): 0.5394920 object centre (A): 12.99900 40.19700 64.38150 number of atom coordinates read : 4760 total number of charged atoms : 4601 net assigned charge : 3.200007 assigned positive charge : 717.2185 centred at (gu) : 90.28871 90.94591 89.54134 assigned negative charge : -714.0231 centred at (gu) : 90.21420 90.94921 89.55128 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8873 nv = 96 ne = 84 npr = 97300 no. pairs analyzed = 97300 no. exposed pairs = 5770 no. arc points = 39109 no. surface atoms = 1936 nbur = 2824 mkacc time = 0.1600000 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 = 1.596000 m= 353 mr = 4875 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3100000 number of dielectric boundary points 4327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3984 ## 538 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 11827 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6289285E-10 6.2055673E-11 midg,1,midg; midg,igrid,midg 1.4255870E-10 1.5619310E-10 1,midg,midg; igrid,midg,midg -4.4171050E-10 8.2593821E-10 gauss-seidel spectral radius is 0.9824187 estimated iterations to convergence 62 setup time was (sec) 0.5100000 now iterating at: 16:02:40 rms-change max change #iterations 8.9478076E-02 13.86801 at 10iterations 5.9824935E-03 0.9459000 at 20iterations 5.9575879E-04 0.1116486 at 30iterations 1.6299264E-04 3.1246185E-02 at 40iterations 6.1867315E-05 9.9086761E-03 at 50iterations finished qdiffx linear iterations at : 16:02:43 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 6.1867315E-05 9.9086761E-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 16:02:43 3.538u 0.171s 0:04.28 86.4% 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 16:02:43 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4760 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN9 975 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.618476 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): -19.99500 45.99300 ymin,ymax (A): 8.247999 72.14600 zmin,zma (A): 33.89900 94.86400 x,y,z range (A): 65.98800 63.89800 60.96500 scale (grids/A): 1.618476 object centre (A): 12.99900 40.19700 64.38150 number of atom coordinates read : 4760 total number of charged atoms : 4601 net assigned charge : 3.200007 assigned positive charge : 717.2185 centred at (gu) : 90.86427 92.83646 88.62248 assigned negative charge : -714.0231 centred at (gu) : 90.64201 92.84729 88.65298 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 99864 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39109 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31790 mr = 70782 m= 3411 mr = 22349 m= 92 mr = 1716 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 575 time to turn everything in is 0.5000000 number of dielectric boundary points 40307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 416 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 35081 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) : 0.5394920 object centre at (A) : 12.99900 40.19700 64.38150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0674227E-03 1.1880155E-02 midg,1,midg; midg,igrid,midg -5.1055378E-03 -1.4642255E-02 1,midg,midg; igrid,midg,midg -3.1100942E-02 2.1706676E-02 gauss-seidel spectral radius is 0.9983274 estimated iterations to convergence 194 setup time was (sec) 0.7200000 now iterating at: 16:02:44 rms-change max change #iterations 4.296269 166.1893 at 10iterations 1.853951 64.44589 at 20iterations 0.8003400 22.40136 at 30iterations 0.3464822 10.79639 at 40iterations 0.1494009 4.471414 at 50iterations 6.4700909E-02 1.761708 at 60iterations 2.8031766E-02 0.8160057 at 70iterations 1.2195375E-02 0.3635559 at 80iterations 5.3048865E-03 0.1509218 at 90iterations 2.3299446E-03 7.1372986E-02 at 100iterations 1.0504363E-03 3.3163071E-02 at 110iterations 5.0157972E-04 1.6716003E-02 at 120iterations finished qdiffx linear iterations at : 16:02:51 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 5.0157972E-04 1.6716003E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 16:02:52 8.119u 0.195s 0:08.69 95.5% 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 16:02:52 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4760 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ASP 610 has a net charge of -2.0000 !!! WARNING: ZN9 975 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.427714 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): -19.99500 45.99300 ymin,ymax (A): 8.247999 72.14600 zmin,zma (A): 33.89900 94.86400 x,y,z range (A): 65.98800 63.89800 60.96500 scale (grids/A): 2.427714 object centre (A): 12.99900 40.19700 64.38150 number of atom coordinates read : 4760 total number of charged atoms : 4601 net assigned charge : 3.200007 assigned positive charge : 717.2185 centred at (gu) : 91.29610 94.25410 87.93333 assigned negative charge : -714.0231 centred at (gu) : 90.96298 94.27073 87.97945 start vw surface at 0.1200000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 232629 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39109 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 110709 mr = 173567 m= 32142 mr = 88433 m= 5262 mr = 24398 m= 359 mr = 3474 m= 2 mr = 167 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 1936 time to turn everything in is 1.190000 number of dielectric boundary points 91064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 36760 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) : 1.618476 object centre at (A) : 12.99900 40.19700 64.38150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7388618E-02 0.1754634 midg,1,midg; midg,igrid,midg -0.1355387 -0.3159778 1,midg,midg; igrid,midg,midg -0.5605561 0.2844894 gauss-seidel spectral radius is 0.9992202 estimated iterations to convergence 283 setup time was (sec) 1.430000 now iterating at: 16:02:54 rms-change max change #iterations 11.14535 300.9595 at 10iterations 6.508778 143.0190 at 20iterations 3.770921 78.11865 at 30iterations 2.184150 47.85026 at 40iterations 1.257321 23.55524 at 50iterations 0.7228826 14.30731 at 60iterations 0.4132474 8.260993 at 70iterations 0.2360744 4.325550 at 80iterations 0.1350863 2.487633 at 90iterations 7.7003218E-02 1.347788 at 100iterations 4.3946914E-02 0.7446022 at 110iterations 2.5062257E-02 0.4097698 at 120iterations 1.4254642E-02 0.2539825 at 130iterations 8.1354575E-03 0.1353588 at 140iterations 4.6508475E-03 8.6671829E-02 at 150iterations 2.6777752E-03 4.6558857E-02 at 160iterations 1.5609775E-03 2.6856422E-02 at 170iterations 9.3176996E-04 1.5216827E-02 at 180iterations finished qdiffx linear iterations at : 16:03:05 total time elapsed so far: 12.97000 # loops : 180 mean,max change (kT/e) : 9.3176996E-04 1.5216827E-02 energy calculations done at 12.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 16:03:06 13.103u 0.205s 0:13.79 96.4% 0+0k 0+0io 0pf+0w