Wed Dec 21 14:22:39 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 14:22:42 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 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: 0.6459339 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): -4.467000 34.59300 ymin,ymax (A): -3.578000 49.09700 zmin,zma (A): -24.19900 30.91500 x,y,z range (A): 39.06000 52.67500 55.11400 scale (grids/A): 0.6459339 object centre (A): 15.06300 22.75950 3.358001 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 6.0006887E-02 assigned positive charge : 287.8521 centred at (gu) : 90.47281 92.30047 90.06982 assigned negative charge : -287.7922 centred at (gu) : 90.53146 92.42418 90.04242 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5602 nv = 96 ne = 84 npr = 40154 no. pairs analyzed = 40154 no. exposed pairs = 2417 no. arc points = 16831 no. surface atoms = 827 nbur = 1119 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 273 mr = 3143 m= 0 mr = 42 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.2700000 number of dielectric boundary points 2690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1607 ## 132 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6426 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2710140E-09 3.2689340E-09 midg,1,midg; midg,igrid,midg 7.8229183E-09 -2.0199213E-08 1,midg,midg; igrid,midg,midg 5.7278045E-09 -6.0804344E-09 gauss-seidel spectral radius is 0.9875222 estimated iterations to convergence 73 setup time was (sec) 0.6900000 now iterating at: 14:22:43 rms-change max change #iterations 0.1322469 23.52809 at 10iterations 1.3308969E-02 2.388527 at 20iterations 1.3434428E-03 0.1922607 at 30iterations 1.3353351E-04 2.1297455E-02 at 40iterations 1.3680358E-05 2.1181107E-03 at 50iterations finished qdiffx linear iterations at : 14:22:50 total time elapsed so far: 7.550000 # loops : 50 mean,max change (kT/e) : 1.3680358E-05 2.1181107E-03 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 14:22:58 7.734u 0.515s 0:17.05 48.3% 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 14:23:00 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 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: 1.937802 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): -4.467000 34.59300 ymin,ymax (A): -3.578000 49.09700 zmin,zma (A): -24.19900 30.91500 x,y,z range (A): 39.06000 52.67500 55.11400 scale (grids/A): 1.937802 object centre (A): 15.06300 22.75950 3.358001 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 6.0006887E-02 assigned positive charge : 287.8521 centred at (gu) : 91.41849 96.90124 90.20946 assigned negative charge : -287.7922 centred at (gu) : 91.59456 97.27258 90.12730 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 59716 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16831 grid for indexing accessible points = 1.400000 m= 21945 mr = 41494 m= 3280 mr = 16785 m= 153 mr = 2142 m= 0 mr = 49 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1446 time to turn everything in is 0.5300000 number of dielectric boundary points 24624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 88 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 14332 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) : 0.6459339 object centre at (A) : 15.06300 22.75950 3.358001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5169335E-02 8.9702914E-03 midg,1,midg; midg,igrid,midg 2.1662127E-02 -1.8248744E-02 1,midg,midg; igrid,midg,midg 3.0794004E-03 -4.9119769E-03 gauss-seidel spectral radius is 0.9985993 estimated iterations to convergence 212 setup time was (sec) 0.9900000 now iterating at: 14:23:02 rms-change max change #iterations 3.716646 179.5393 at 10iterations 1.716583 67.48410 at 20iterations 0.7991184 30.33241 at 30iterations 0.3718446 14.51434 at 40iterations 0.1717464 6.432114 at 50iterations 7.9317339E-02 2.707397 at 60iterations 3.6639523E-02 1.462536 at 70iterations 1.7105319E-02 0.6004996 at 80iterations 7.9090744E-03 0.2775097 at 90iterations 3.6772937E-03 0.1289644 at 100iterations 1.6990127E-03 6.0913086E-02 at 110iterations 7.8950421E-04 2.5848389E-02 at 120iterations finished qdiffx linear iterations at : 14:23:20 total time elapsed so far: 18.99000 # loops : 120 mean,max change (kT/e) : 7.8950421E-04 2.5848389E-02 energy calculations done at 18.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.17000 DelPhi exited at 14:23:21 19.171u 0.655s 0:21.20 93.4% 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 Wed Dec 21 2011 at 14:23:22 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1946 !!! WARNING: ARG 41 has a net charge of 0.0400 !!! WARNING: LYS 155 has a net charge of 0.0200 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: 2.906703 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): -4.467000 34.59300 ymin,ymax (A): -3.578000 49.09700 zmin,zma (A): -24.19900 30.91500 x,y,z range (A): 39.06000 52.67500 55.11400 scale (grids/A): 2.906703 object centre (A): 15.06300 22.75950 3.358001 number of atom coordinates read : 1946 total number of charged atoms : 1814 net assigned charge : 6.0006887E-02 assigned positive charge : 287.8521 centred at (gu) : 92.12762 100.3519 90.31414 assigned negative charge : -287.7922 centred at (gu) : 92.39188 100.9089 90.19097 start vw surface at 0.1100000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 137960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16831 grid for indexing accessible points = 1.400000 m= 70942 mr = 100283 m= 25732 mr = 59102 m= 5934 mr = 21374 m= 730 mr = 4576 m= 35 mr = 474 m= 0 mr = 10 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 5133 time to turn everything in is 1.270000 number of dielectric boundary points 55514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 14506 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) : 1.937802 object centre at (A) : 15.06300 22.75950 3.358001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.098770 1.9349270E-03 midg,1,midg; midg,igrid,midg 0.1761376 -0.2218160 1,midg,midg; igrid,midg,midg 2.0164829E-02 -3.0237088E-02 gauss-seidel spectral radius is 0.9992343 estimated iterations to convergence 285 setup time was (sec) 1.600000 now iterating at: 14:23:24 rms-change max change #iterations 8.673942 357.4410 at 10iterations 4.982835 125.6760 at 20iterations 2.842596 66.54066 at 30iterations 1.622193 37.87636 at 40iterations 0.9252147 20.27806 at 50iterations 0.5251737 10.97439 at 60iterations 0.3001093 8.094849 at 70iterations 0.1703782 3.732030 at 80iterations 9.7094230E-02 2.024652 at 90iterations 5.5143125E-02 1.231024 at 100iterations 3.1377409E-02 0.6568727 at 110iterations 1.7815571E-02 0.3801699 at 120iterations 1.0115630E-02 0.2164230 at 130iterations 5.7469942E-03 0.1172485 at 140iterations 3.2672011E-03 6.7577362E-02 at 150iterations 1.8552184E-03 3.7578583E-02 at 160iterations 1.0544101E-03 2.2846222E-02 at 170iterations 6.0069794E-04 1.1905670E-02 at 180iterations finished qdiffx linear iterations at : 14:23:53 total time elapsed so far: 30.85000 # loops : 180 mean,max change (kT/e) : 6.0069794E-04 1.1905670E-02 energy calculations done at 30.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 31.03000 DelPhi exited at 14:23:54 31.031u 0.562s 0:32.19 98.1% 0+0k 0+0io 0pf+0w