Tue Oct 11 08:11:14 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 Tue Oct 11 2011 at 08:11:14 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1806 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: GLM 165 has a net charge of -0.0940 !!! WARNING: HIZ 166 has a net charge of 0.2000 !!! WARNING: ZN4 400 has a net charge of 1.4000 !!! WARNING: ZN4 401 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7270796 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): -17.00200 31.96100 ymin,ymax (A): 18.37000 63.44100 zmin,zma (A): -22.85200 26.03800 x,y,z range (A): 48.96300 45.07100 48.89000 scale (grids/A): 0.7270796 object centre (A): 7.479500 40.90550 1.593000 number of atom coordinates read : 1806 total number of charged atoms : 1662 net assigned charge : 4.606002 assigned positive charge : 262.8894 centred at (gu) : 91.18785 91.74062 89.19990 assigned negative charge : -258.2833 centred at (gu) : 91.14285 91.85141 89.25225 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6822 nv = 96 ne = 84 npr = 34486 no. pairs analyzed = 34486 no. exposed pairs = 2724 no. arc points = 20025 no. surface atoms = 905 nbur = 901 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 3172 m= 8 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 4071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1568 ## 117 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6996 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0928267E-07 2.5068706E-08 midg,1,midg; midg,igrid,midg 9.3746763E-08 -1.3566215E-08 1,midg,midg; igrid,midg,midg 2.7165335E-08 1.1188133E-07 gauss-seidel spectral radius is 0.9901314 estimated iterations to convergence 82 setup time was (sec) 0.5100000 now iterating at: 08:11:14 rms-change max change #iterations 0.2143973 28.82762 at 10iterations 2.6999308E-02 3.567394 at 20iterations 3.4760674E-03 0.5673218 at 30iterations 4.5200248E-04 7.0673943E-02 at 40iterations 5.7096444E-05 8.4125996E-03 at 50iterations finished qdiffx linear iterations at : 08:11:18 total time elapsed so far: 4.120000 # loops : 50 mean,max change (kT/e) : 5.7096444E-05 8.4125996E-03 energy calculations done at 4.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.310000 DelPhi exited at 08:11:19 4.315u 0.258s 0:05.03 90.6% 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 Tue Oct 11 2011 at 08:11:19 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1806 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: GLM 165 has a net charge of -0.0940 !!! WARNING: HIZ 166 has a net charge of 0.2000 !!! WARNING: ZN4 400 has a net charge of 1.4000 !!! WARNING: ZN4 401 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.181239 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): -17.00200 31.96100 ymin,ymax (A): 18.37000 63.44100 zmin,zma (A): -22.85200 26.03800 x,y,z range (A): 48.96300 45.07100 48.89000 scale (grids/A): 2.181239 object centre (A): 7.479500 40.90550 1.593000 number of atom coordinates read : 1806 total number of charged atoms : 1662 net assigned charge : 4.606002 assigned positive charge : 262.8894 centred at (gu) : 93.56376 95.22207 87.60011 assigned negative charge : -258.2833 centred at (gu) : 93.42867 95.55423 87.75683 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 70846 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20025 grid for indexing accessible points = 1.400000 m= 24893 mr = 43797 m= 4558 mr = 16886 m= 364 mr = 2514 m= 7 mr = 122 m= 0 mr = 2 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 37347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 13231 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) : 0.7270796 object centre at (A) : 7.479500 40.90550 1.593000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3312769E-02 -1.5928283E-02 midg,1,midg; midg,igrid,midg 3.3252466E-02 2.7489850E-02 1,midg,midg; igrid,midg,midg -6.3689356E-04 -5.4987706E-03 gauss-seidel spectral radius is 0.9988905 estimated iterations to convergence 238 setup time was (sec) 0.9500000 now iterating at: 08:11:20 rms-change max change #iterations 4.515180 213.6856 at 10iterations 2.274051 77.37470 at 20iterations 1.157043 40.03513 at 30iterations 0.5840501 19.80872 at 40iterations 0.2956259 9.136564 at 50iterations 0.1497173 4.299762 at 60iterations 7.5454496E-02 2.855244 at 70iterations 3.8199935E-02 1.178825 at 80iterations 1.9253440E-02 0.5688171 at 90iterations 9.6948529E-03 0.3088207 at 100iterations 4.8985113E-03 0.1564598 at 110iterations 2.4723480E-03 7.5760841E-02 at 120iterations finished qdiffx linear iterations at : 08:11:29 total time elapsed so far: 9.810000 # loops : 120 mean,max change (kT/e) : 2.4723480E-03 7.5760841E-02 energy calculations done at 9.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.00000 DelPhi exited at 08:11:30 10.007u 0.325s 0:11.07 93.2% 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 Tue Oct 11 2011 at 08:11:30 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1806 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: GLM 165 has a net charge of -0.0940 !!! WARNING: HIZ 166 has a net charge of 0.2000 !!! WARNING: ZN4 400 has a net charge of 1.4000 !!! WARNING: ZN4 401 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.271858 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): -17.00200 31.96100 ymin,ymax (A): 18.37000 63.44100 zmin,zma (A): -22.85200 26.03800 x,y,z range (A): 48.96300 45.07100 48.89000 scale (grids/A): 3.271858 object centre (A): 7.479500 40.90550 1.593000 number of atom coordinates read : 1806 total number of charged atoms : 1662 net assigned charge : 4.606002 assigned positive charge : 262.8894 centred at (gu) : 95.34569 97.83325 86.40024 assigned negative charge : -258.2833 centred at (gu) : 95.14310 98.33147 86.63536 start vw surface at 0.1600000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 162893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20025 grid for indexing accessible points = 1.400000 m= 77944 mr = 107013 m= 30002 mr = 60146 m= 8109 mr = 22580 m= 1374 mr = 5572 m= 117 mr = 829 m= 5 mr = 60 m= 0 mr = 2 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.830000 number of dielectric boundary points 84242 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 13296 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) : 2.181239 object centre at (A) : 7.479500 40.90550 1.593000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6118686 -0.2623373 midg,1,midg; midg,igrid,midg 0.1790801 0.2107020 1,midg,midg; igrid,midg,midg -0.1159868 4.5257088E-02 gauss-seidel spectral radius is 0.9993579 estimated iterations to convergence 311 setup time was (sec) 2.170000 now iterating at: 08:11:32 rms-change max change #iterations 10.17468 362.2753 at 10iterations 6.245372 158.1654 at 20iterations 3.793628 93.49072 at 30iterations 2.305918 55.76821 at 40iterations 1.397502 28.91757 at 50iterations 0.8426281 17.53463 at 60iterations 0.5086343 9.691248 at 70iterations 0.3050722 5.595692 at 80iterations 0.1832929 3.555149 at 90iterations 0.1101525 2.201862 at 100iterations 6.5984726E-02 1.334654 at 110iterations 3.9502133E-02 0.8323269 at 120iterations 2.3682900E-02 0.4572830 at 130iterations 1.4139229E-02 0.2799397 at 140iterations 8.4804446E-03 0.1487885 at 150iterations 5.0657652E-03 9.3506575E-02 at 160iterations 3.0298184E-03 5.5689812E-02 at 170iterations 1.8095733E-03 3.3020020E-02 at 180iterations finished qdiffx linear iterations at : 08:11:46 total time elapsed so far: 15.89000 # loops : 180 mean,max change (kT/e) : 1.8095733E-03 3.3020020E-02 energy calculations done at 15.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.07000 DelPhi exited at 08:11:47 16.069u 0.285s 0:16.69 97.9% 0+0k 0+0io 0pf+0w