Wed Dec 21 14:21:10 PST 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 Wed Dec 21 2011 at 14:21:11 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6497180 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): -5.354000 33.90200 ymin,ymax (A): -3.317000 46.65500 zmin,zma (A): -7.936000 46.85700 x,y,z range (A): 39.25600 49.97200 54.79300 scale (grids/A): 0.6497180 object centre (A): 14.27400 21.66900 19.46050 number of atom coordinates read : 1958 total number of charged atoms : 1762 net assigned charge : -18.57600 assigned positive charge : 267.9864 centred at (gu) : 89.50359 92.92677 89.86293 assigned negative charge : -286.5622 centred at (gu) : 89.44906 93.02865 89.92075 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5601 nv = 96 ne = 84 npr = 40903 no. pairs analyzed = 40903 no. exposed pairs = 2465 no. arc points = 17196 no. surface atoms = 837 nbur = 1121 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 290 mr = 3156 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.1600000 number of dielectric boundary points 2708 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1563 ## 106 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6385 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9300459E-08 -4.0149310E-08 midg,1,midg; midg,igrid,midg -1.3414366E-08 -8.5542140E-08 1,midg,midg; igrid,midg,midg -4.5326082E-08 -2.6132254E-08 gauss-seidel spectral radius is 0.9876653 estimated iterations to convergence 74 setup time was (sec) 0.3700000 now iterating at: 14:21:11 rms-change max change #iterations 0.1378464 21.58886 at 10iterations 1.4064240E-02 2.303674 at 20iterations 1.4387209E-03 0.2237625 at 30iterations 1.5017934E-04 2.3694992E-02 at 40iterations 1.5172310E-05 2.2735596E-03 at 50iterations finished qdiffx linear iterations at : 14:21:14 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 1.5172310E-05 2.2735596E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 14:21:15 3.496u 0.276s 0:04.87 77.2% 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 Wed Dec 21 2011 at 14:21:16 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.949154 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): -5.354000 33.90200 ymin,ymax (A): -3.317000 46.65500 zmin,zma (A): -7.936000 46.85700 x,y,z range (A): 39.25600 49.97200 54.79300 scale (grids/A): 1.949154 object centre (A): 14.27400 21.66900 19.46050 number of atom coordinates read : 1958 total number of charged atoms : 1762 net assigned charge : -18.57600 assigned positive charge : 267.9864 centred at (gu) : 88.51104 98.78053 89.58896 assigned negative charge : -286.5622 centred at (gu) : 88.34744 99.08611 89.76225 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 60591 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17196 grid for indexing accessible points = 1.400000 m= 21159 mr = 41995 m= 2834 mr = 15896 m= 145 mr = 1724 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 649 time to turn everything in is 0.3100000 number of dielectric boundary points 25072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 13800 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) : 0.6497180 object centre at (A) : 14.27400 21.66900 19.46050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5227175E-02 8.1609664E-03 midg,1,midg; midg,igrid,midg -1.0817978E-02 -0.1033977 1,midg,midg; igrid,midg,midg -2.9217543E-02 -1.9091722E-02 gauss-seidel spectral radius is 0.9986142 estimated iterations to convergence 213 setup time was (sec) 0.5600000 now iterating at: 14:21:17 rms-change max change #iterations 3.760374 199.6943 at 10iterations 1.750829 71.09312 at 20iterations 0.8143063 29.62391 at 30iterations 0.3804875 14.09192 at 40iterations 0.1760190 6.165277 at 50iterations 8.1905216E-02 3.004120 at 60iterations 3.8341120E-02 1.401472 at 70iterations 1.7824458E-02 0.6503983 at 80iterations 8.3038444E-03 0.3043041 at 90iterations 3.8626189E-03 0.1374084 at 100iterations 1.7923820E-03 7.1722031E-02 at 110iterations 8.3588297E-04 3.6994934E-02 at 120iterations finished qdiffx linear iterations at : 14:21:24 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 8.3588297E-04 3.6994934E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 14:21:32 8.005u 0.308s 0:16.66 49.8% 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 Wed Dec 21 2011 at 14:21:35 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1958 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.923731 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): -5.354000 33.90200 ymin,ymax (A): -3.317000 46.65500 zmin,zma (A): -7.936000 46.85700 x,y,z range (A): 39.25600 49.97200 54.79300 scale (grids/A): 2.923731 object centre (A): 14.27400 21.66900 19.46050 number of atom coordinates read : 1958 total number of charged atoms : 1762 net assigned charge : -18.57600 assigned positive charge : 267.9864 centred at (gu) : 87.76668 103.1708 89.38348 assigned negative charge : -286.5622 centred at (gu) : 87.52122 103.6292 89.64339 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 139952 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17196 grid for indexing accessible points = 1.400000 m= 69860 mr = 101290 m= 23504 mr = 57897 m= 4935 mr = 19130 m= 610 mr = 3642 m= 43 mr = 390 m= 0 mr = 22 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 2331 time to turn everything in is 0.8000000 number of dielectric boundary points 56533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14087 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) : 1.949154 object centre at (A) : 14.27400 21.66900 19.46050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6571873 0.7171286 midg,1,midg; midg,igrid,midg -2.7889118E-02 -1.060712 1,midg,midg; igrid,midg,midg -0.2349809 -0.1748441 gauss-seidel spectral radius is 0.9992417 estimated iterations to convergence 287 setup time was (sec) 1.020000 now iterating at: 14:21:38 rms-change max change #iterations 8.727063 414.6887 at 10iterations 5.046536 157.5117 at 20iterations 2.894105 69.85831 at 30iterations 1.657575 38.05948 at 40iterations 0.9502243 29.74479 at 50iterations 0.5435664 12.74485 at 60iterations 0.3097836 6.671860 at 70iterations 0.1766500 3.466400 at 80iterations 0.1006653 2.073938 at 90iterations 5.7449374E-02 1.430485 at 100iterations 3.2701027E-02 0.6719234 at 110iterations 1.8671555E-02 0.3754349 at 120iterations 1.0649430E-02 0.2101593 at 130iterations 6.0551912E-03 0.1328402 at 140iterations 3.4474591E-03 6.9293976E-02 at 150iterations 1.9680057E-03 3.9165020E-02 at 160iterations 1.1186918E-03 2.1438599E-02 at 170iterations 6.3878240E-04 1.3652802E-02 at 180iterations finished qdiffx linear iterations at : 14:21:50 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 6.3878240E-04 1.3652802E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.84000 DelPhi exited at 14:21:59 12.845u 0.284s 0:24.37 53.8% 0+0k 0+0io 0pf+0w