Sat Oct 8 14:24:27 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 Sat Oct 8 2011 at 14:24:27 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3024 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6412681 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): -12.26300 43.25200 ymin,ymax (A): -22.26900 22.52100 zmin,zma (A): -7.499000 46.85300 x,y,z range (A): 55.51500 44.79000 54.35200 scale (grids/A): 0.6412681 object centre (A): 15.49450 0.1259995 19.67700 number of atom coordinates read : 3024 total number of charged atoms : 2877 net assigned charge : -0.9859930 assigned positive charge : 454.1536 centred at (gu) : 88.78701 89.54657 91.68906 assigned negative charge : -455.1403 centred at (gu) : 88.75266 89.45151 91.63459 start vw surface at 0.1400000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8219 nv = 96 ne = 84 npr = 63537 no. pairs analyzed = 63537 no. exposed pairs = 3420 no. arc points = 23980 no. surface atoms = 1158 nbur = 1866 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 421 mr = 4805 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3792 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2314 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10008 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.4150059E-09 8.9594012E-09 midg,1,midg; midg,igrid,midg -1.6575942E-08 1.0663679E-08 1,midg,midg; igrid,midg,midg -8.2498248E-09 2.5520812E-09 gauss-seidel spectral radius is 0.9874317 estimated iterations to convergence 73 setup time was (sec) 0.6700000 now iterating at: 14:24:28 rms-change max change #iterations 0.1615999 21.90998 at 10iterations 1.6595704E-02 2.232512 at 20iterations 1.6994854E-03 0.2474594 at 30iterations 1.9689578E-04 2.7935028E-02 at 40iterations 2.7204531E-05 3.8223267E-03 at 50iterations finished qdiffx linear iterations at : 14:24:32 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 2.7204531E-05 3.8223267E-03 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.510000 DelPhi exited at 14:24:32 4.515u 0.373s 0:05.17 94.3% 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 Sat Oct 8 2011 at 14:24:32 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3024 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.923804 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): -12.26300 43.25200 ymin,ymax (A): -22.26900 22.52100 zmin,zma (A): -7.499000 46.85300 x,y,z range (A): 55.51500 44.79000 54.35200 scale (grids/A): 1.923804 object centre (A): 15.49450 0.1259995 19.67700 number of atom coordinates read : 3024 total number of charged atoms : 2877 net assigned charge : -0.9859930 assigned positive charge : 454.1536 centred at (gu) : 86.36041 88.63939 95.06635 assigned negative charge : -455.1403 centred at (gu) : 86.25785 88.35422 94.90337 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89756 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23980 grid for indexing accessible points = 1.400000 m= 32179 mr = 64873 m= 4695 mr = 24110 m= 281 mr = 2842 m= 10 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 393 time to turn everything in is 0.6900000 number of dielectric boundary points 34992 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 151 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 22631 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) : 0.6412681 object centre at (A) : 15.49450 0.1259995 19.67700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8010831E-02 9.2780609E-03 midg,1,midg; midg,igrid,midg -1.6242688E-03 2.1817882E-02 1,midg,midg; igrid,midg,midg -4.2059179E-02 6.0181008E-03 gauss-seidel spectral radius is 0.9986946 estimated iterations to convergence 219 setup time was (sec) 0.9900000 now iterating at: 14:24:34 rms-change max change #iterations 4.738255 219.9436 at 10iterations 2.271257 75.59815 at 20iterations 1.081119 34.90869 at 30iterations 0.5153571 17.20175 at 40iterations 0.2464577 6.752140 at 50iterations 0.1173684 3.228129 at 60iterations 5.6035277E-02 1.660610 at 70iterations 2.6806353E-02 0.7845688 at 80iterations 1.2825958E-02 0.3500824 at 90iterations 6.1142705E-03 0.1671000 at 100iterations 2.9174979E-03 8.7631226E-02 at 110iterations 1.3956653E-03 3.7357330E-02 at 120iterations finished qdiffx linear iterations at : 14:24:43 total time elapsed so far: 10.60000 # loops : 120 mean,max change (kT/e) : 1.3956653E-03 3.7357330E-02 energy calculations done at 10.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.77000 DelPhi exited at 14:24:44 10.772u 0.459s 0:11.52 97.3% 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 Sat Oct 8 2011 at 14:24:44 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3024 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NAP 500 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.885706 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): -12.26300 43.25200 ymin,ymax (A): -22.26900 22.52100 zmin,zma (A): -7.499000 46.85300 x,y,z range (A): 55.51500 44.79000 54.35200 scale (grids/A): 2.885706 object centre (A): 15.49450 0.1259995 19.67700 number of atom coordinates read : 3024 total number of charged atoms : 2877 net assigned charge : -0.9859930 assigned positive charge : 454.1536 centred at (gu) : 84.54049 87.95896 97.59944 assigned negative charge : -455.1403 centred at (gu) : 84.38663 87.53127 97.35511 start vw surface at 0.1200000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 207708 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23980 grid for indexing accessible points = 1.400000 m= 106161 mr = 156526 m= 36933 mr = 88313 m= 8362 mr = 29621 m= 1153 mr = 6141 m= 65 mr = 722 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 1373 time to turn everything in is 1.870000 number of dielectric boundary points 79024 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.000000 number of grid points assigned charge 23011 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) : 1.923804 object centre at (A) : 15.49450 0.1259995 19.67700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9856724E-02 0.2862734 midg,1,midg; midg,igrid,midg 7.0104664E-03 0.2455156 1,midg,midg; igrid,midg,midg -0.5865598 0.1515966 gauss-seidel spectral radius is 0.9992774 estimated iterations to convergence 294 setup time was (sec) 2.190000 now iterating at: 14:24:46 rms-change max change #iterations 11.00778 451.7371 at 10iterations 6.453090 149.2613 at 20iterations 3.751002 67.91141 at 30iterations 2.187648 40.40425 at 40iterations 1.266990 20.47883 at 50iterations 0.7371203 14.17521 at 60iterations 0.4270155 7.360544 at 70iterations 0.2471413 4.067997 at 80iterations 0.1436080 2.408808 at 90iterations 8.3033107E-02 1.352320 at 100iterations 4.7997594E-02 0.7754545 at 110iterations 2.7763272E-02 0.4314537 at 120iterations 1.6106399E-02 0.2754593 at 130iterations 9.3223583E-03 0.1476479 at 140iterations 5.4118792E-03 8.6025238E-02 at 150iterations 3.1356914E-03 5.2543640E-02 at 160iterations 1.8234936E-03 2.8945923E-02 at 170iterations 1.0622033E-03 1.6770363E-02 at 180iterations finished qdiffx linear iterations at : 14:25:03 total time elapsed so far: 18.42000 # loops : 180 mean,max change (kT/e) : 1.0622033E-03 1.6770363E-02 energy calculations done at 18.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.59000 DelPhi exited at 14:25:03 18.597u 0.489s 0:19.36 98.5% 0+0k 0+0io 0pf+0w