Mon Oct 10 17:08:19 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 17:08:19 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4306 !!! WARNING: GLM 169 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5614522 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): -15.90600 36.45600 ymin,ymax (A): -31.12600 32.28100 zmin,zma (A): -3.999000 58.09700 x,y,z range (A): 52.36200 63.40700 62.09600 scale (grids/A): 0.5614522 object centre (A): 10.27500 0.5775013 27.04900 number of atom coordinates read : 4306 total number of charged atoms : 4142 net assigned charge : -0.5939775 assigned positive charge : 650.3632 centred at (gu) : 90.21958 90.48047 89.31271 assigned negative charge : -650.9611 centred at (gu) : 90.07012 90.54037 89.39497 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8852 nv = 96 ne = 84 npr = 86452 no. pairs analyzed = 86452 no. exposed pairs = 5713 no. arc points = 39324 no. surface atoms = 1912 nbur = 2394 mkacc time = 0.1800000 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 = 1.540000 m= 407 mr = 4587 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 4651 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3950 ## 462 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 11570 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5593457E-09 -1.2643916E-09 midg,1,midg; midg,igrid,midg 8.3567797E-10 -1.2452716E-09 1,midg,midg; igrid,midg,midg -2.5362039E-09 2.5665452E-09 gauss-seidel spectral radius is 0.9837421 estimated iterations to convergence 64 setup time was (sec) 0.6100000 now iterating at: 17:08:19 rms-change max change #iterations 0.1030077 14.69487 at 10iterations 7.5467029E-03 1.159588 at 20iterations 5.9793075E-04 8.5060120E-02 at 30iterations 9.8697790E-05 1.3105392E-02 at 40iterations 3.2193824E-05 3.9343834E-03 at 50iterations finished qdiffx linear iterations at : 17:08:22 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 3.2193824E-05 3.9343834E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 17:08:22 3.241u 0.149s 0:03.76 89.8% 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 Mon Oct 10 2011 at 17:08:22 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4306 !!! WARNING: GLM 169 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.684357 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): -15.90600 36.45600 ymin,ymax (A): -31.12600 32.28100 zmin,zma (A): -3.999000 58.09700 x,y,z range (A): 52.36200 63.40700 62.09600 scale (grids/A): 1.684357 object centre (A): 10.27500 0.5775013 27.04900 number of atom coordinates read : 4306 total number of charged atoms : 4142 net assigned charge : -0.5939775 assigned positive charge : 650.3632 centred at (gu) : 90.65725 91.43970 87.93684 assigned negative charge : -650.9611 centred at (gu) : 90.21011 91.62080 88.18439 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 98031 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39324 grid for indexing accessible points = 1.400000 m= 31576 mr = 67075 m= 3713 mr = 21469 m= 135 mr = 1799 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 43089 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 392 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 31942 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) : 0.5614522 object centre at (A) : 10.27500 0.5775013 27.04900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7106715E-03 -8.9622019E-03 midg,1,midg; midg,igrid,midg -1.1363494E-02 -2.9329160E-02 1,midg,midg; igrid,midg,midg -1.1649366E-02 2.1541839E-02 gauss-seidel spectral radius is 0.9984417 estimated iterations to convergence 201 setup time was (sec) 0.9100000 now iterating at: 17:08:24 rms-change max change #iterations 4.450755 175.0473 at 10iterations 1.971897 69.40701 at 20iterations 0.8768601 30.25558 at 30iterations 0.3891941 11.52189 at 40iterations 0.1736904 4.813908 at 50iterations 7.7400759E-02 2.471214 at 60iterations 3.4325279E-02 1.001538 at 70iterations 1.5317056E-02 0.4346008 at 80iterations 6.8174838E-03 0.2213821 at 90iterations 3.0479063E-03 9.2073202E-02 at 100iterations 1.3586254E-03 4.1777611E-02 at 110iterations 6.1310316E-04 1.7847061E-02 at 120iterations finished qdiffx linear iterations at : 17:08:30 total time elapsed so far: 6.980000 # loops : 120 mean,max change (kT/e) : 6.1310316E-04 1.7847061E-02 energy calculations done at 6.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.160000 DelPhi exited at 17:08:30 7.164u 0.171s 0:07.71 95.0% 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 17:08:30 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4306 !!! WARNING: GLM 169 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.526535 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): -15.90600 36.45600 ymin,ymax (A): -31.12600 32.28100 zmin,zma (A): -3.999000 58.09700 x,y,z range (A): 52.36200 63.40700 62.09600 scale (grids/A): 2.526535 object centre (A): 10.27500 0.5775013 27.04900 number of atom coordinates read : 4306 total number of charged atoms : 4142 net assigned charge : -0.5939775 assigned positive charge : 650.3632 centred at (gu) : 90.98545 92.15935 86.90486 assigned negative charge : -650.9611 centred at (gu) : 90.31516 92.43121 87.27654 start vw surface at 0.1700000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 227465 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39324 grid for indexing accessible points = 1.400000 m= 107886 mr = 164069 m= 32313 mr = 84761 m= 5877 mr = 23812 m= 547 mr = 3772 m= 11 mr = 287 m= 0 mr = 2 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.580000 number of dielectric boundary points 97396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 33120 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) : 1.684357 object centre at (A) : 10.27500 0.5775013 27.04900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1363133 -9.7908691E-02 midg,1,midg; midg,igrid,midg -0.5225658 -0.5868974 1,midg,midg; igrid,midg,midg -0.1293532 0.3069918 gauss-seidel spectral radius is 0.9992559 estimated iterations to convergence 289 setup time was (sec) 1.880000 now iterating at: 17:08:32 rms-change max change #iterations 11.36760 315.4642 at 10iterations 6.772458 173.4535 at 20iterations 4.002520 82.59865 at 30iterations 2.347554 46.88435 at 40iterations 1.374587 27.60863 at 50iterations 0.8016090 18.07898 at 60iterations 0.4653458 8.935030 at 70iterations 0.2703064 5.333892 at 80iterations 0.1569261 3.229675 at 90iterations 9.0619944E-02 1.948441 at 100iterations 5.2464396E-02 0.9411030 at 110iterations 3.0208072E-02 0.5593233 at 120iterations 1.7408175E-02 0.3344765 at 130iterations 1.0032803E-02 0.2018089 at 140iterations 5.7864310E-03 0.1099129 at 150iterations 3.3314233E-03 6.3976288E-02 at 160iterations 1.9179570E-03 3.4453392E-02 at 170iterations 1.1037973E-03 1.8421888E-02 at 180iterations finished qdiffx linear iterations at : 17:08:42 total time elapsed so far: 11.57000 # loops : 180 mean,max change (kT/e) : 1.1037973E-03 1.8421888E-02 energy calculations done at 11.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.73000 DelPhi exited at 17:08:43 11.731u 0.179s 0:12.31 96.6% 0+0k 0+0io 0pf+0w