Tue Nov 22 14:10:59 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+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 Tue Nov 22 2011 at 14:11:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6544719 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): -6.294000 34.32100 ymin,ymax (A): -3.365000 48.58800 zmin,zma (A): -23.45700 30.93800 x,y,z range (A): 40.61500 51.95300 54.39500 scale (grids/A): 0.6544719 object centre (A): 14.01350 22.61150 3.740500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.98631 92.44916 89.93434 assigned negative charge : -284.8263 centred at (gu) : 91.08775 92.58157 89.88718 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5675 nv = 96 ne = 84 npr = 40489 no. pairs analyzed = 40489 no. exposed pairs = 2434 no. arc points = 17039 no. surface atoms = 824 nbur = 1140 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 315 mr = 3204 m= 4 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.2100000 number of dielectric boundary points 2748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1724 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 6684 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2276634E-09 1.2810751E-08 midg,1,midg; midg,igrid,midg 1.4093937E-08 -1.6734125E-08 1,midg,midg; igrid,midg,midg 1.5998166E-08 -7.1040653E-09 gauss-seidel spectral radius is 0.9878423 estimated iterations to convergence 74 setup time was (sec) 0.4100000 now iterating at: 14:11:06 rms-change max change #iterations 0.1384496 26.37884 at 10iterations 1.4575064E-02 2.035614 at 20iterations 1.5028885E-03 0.2415571 at 30iterations 1.5295304E-04 2.4290562E-02 at 40iterations 1.6112857E-05 2.3727417E-03 at 50iterations finished qdiffx linear iterations at : 14:11:14 total time elapsed so far: 2.820000 # loops : 50 mean,max change (kT/e) : 1.6112857E-05 2.3727417E-03 energy calculations done at 2.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 2.990000 DelPhi exited at 14:11:16 2.998u 0.146s 0:13.89 22.5% 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 Tue Nov 22 2011 at 14:11:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.963416 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): -6.294000 34.32100 ymin,ymax (A): -3.365000 48.58800 zmin,zma (A): -23.45700 30.93800 x,y,z range (A): 40.61500 51.95300 54.39500 scale (grids/A): 1.963416 object centre (A): 14.01350 22.61150 3.740500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 92.95888 97.34749 89.80308 assigned negative charge : -284.8263 centred at (gu) : 93.26348 97.74491 89.66174 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 61340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17039 grid for indexing accessible points = 1.400000 m= 22577 mr = 42570 m= 3583 mr = 17271 m= 184 mr = 2338 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1228 time to turn everything in is 0.4300000 number of dielectric boundary points 25462 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 14491 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) : 0.6544719 object centre at (A) : 14.01350 22.61150 3.740500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8265178E-02 1.7518893E-02 midg,1,midg; midg,igrid,midg 3.7171252E-02 -6.9796275E-03 1,midg,midg; igrid,midg,midg 1.0182100E-02 -6.6421991E-03 gauss-seidel spectral radius is 0.9986335 estimated iterations to convergence 214 setup time was (sec) 0.7400000 now iterating at: 14:11:19 rms-change max change #iterations 3.771919 212.9483 at 10iterations 1.775245 65.24131 at 20iterations 0.8304482 30.29080 at 30iterations 0.3875976 13.02941 at 40iterations 0.1812106 7.000018 at 50iterations 8.4747992E-02 2.941340 at 60iterations 3.9807942E-02 1.510916 at 70iterations 1.8610332E-02 0.7086334 at 80iterations 8.7171141E-03 0.3076267 at 90iterations 4.0593329E-03 0.1390057 at 100iterations 1.9099792E-03 6.4334869E-02 at 110iterations 8.9211640E-04 2.8533936E-02 at 120iterations finished qdiffx linear iterations at : 14:11:39 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 8.9211640E-04 2.8533936E-02 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 14:11:42 7.064u 0.209s 0:25.20 28.8% 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 Tue Nov 22 2011 at 14:11:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.945124 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): -6.294000 34.32100 ymin,ymax (A): -3.365000 48.58800 zmin,zma (A): -23.45700 30.93800 x,y,z range (A): 40.61500 51.95300 54.39500 scale (grids/A): 2.945124 object centre (A): 14.01350 22.61150 3.740500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 94.43832 101.0212 89.70479 assigned negative charge : -284.8263 centred at (gu) : 94.89533 101.6173 89.49258 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 141501 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17039 grid for indexing accessible points = 1.400000 m= 72254 mr = 102565 m= 26877 mr = 60157 m= 6627 mr = 22310 m= 893 mr = 5148 m= 29 mr = 567 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 4259 time to turn everything in is 1.120000 number of dielectric boundary points 57432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 14656 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) : 1.963416 object centre at (A) : 14.01350 22.61150 3.740500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9164097 6.6788234E-02 midg,1,midg; midg,igrid,midg 0.3496028 -0.1127287 1,midg,midg; igrid,midg,midg 6.9494419E-02 -4.4680774E-02 gauss-seidel spectral radius is 0.9992460 estimated iterations to convergence 287 setup time was (sec) 1.400000 now iterating at: 14:11:49 rms-change max change #iterations 8.734447 363.6661 at 10iterations 5.020847 114.5640 at 20iterations 2.856978 59.00928 at 30iterations 1.631664 31.49777 at 40iterations 0.9327500 19.39888 at 50iterations 0.5312214 9.947532 at 60iterations 0.3030214 5.651686 at 70iterations 0.1726860 3.432249 at 80iterations 9.8455414E-02 2.379496 at 90iterations 5.6101978E-02 1.091928 at 100iterations 3.2001346E-02 0.6233101 at 110iterations 1.8303890E-02 0.3360405 at 120iterations 1.0395283E-02 0.2079968 at 130iterations 5.9269341E-03 0.1423302 at 140iterations 3.3791347E-03 6.9381714E-02 at 150iterations 1.9327445E-03 4.2636871E-02 at 160iterations 1.1016259E-03 2.2323608E-02 at 170iterations 6.2697870E-04 1.2052536E-02 at 180iterations finished qdiffx linear iterations at : 14:12:19 total time elapsed so far: 11.49000 # loops : 180 mean,max change (kT/e) : 6.2697870E-04 1.2052536E-02 energy calculations done at 11.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.67000 DelPhi exited at 14:12:28 11.669u 0.279s 0:44.27 26.9% 0+0k 0+0io 0pf+0w