Sun Oct 9 07:12:46 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 Sun Oct 9 2011 at 07:12:46 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: NAP 191 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6448224 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): -13.20100 38.48100 ymin,ymax (A): -22.20900 29.95500 zmin,zma (A): -15.64200 39.56700 x,y,z range (A): 51.68200 52.16400 55.20900 scale (grids/A): 0.6448224 object centre (A): 12.64000 3.873000 11.96250 number of atom coordinates read : 2004 total number of charged atoms : 1867 net assigned charge : 1.000008 assigned positive charge : 299.9051 centred at (gu) : 90.52956 90.13381 89.24966 assigned negative charge : -298.9052 centred at (gu) : 90.68321 90.04442 89.10979 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5560 nv = 96 ne = 84 npr = 41828 no. pairs analyzed = 41828 no. exposed pairs = 2490 no. arc points = 17860 no. surface atoms = 845 nbur = 1159 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 284 mr = 2956 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 0.2900000 number of dielectric boundary points 2852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1729 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6520 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4888148E-08 1.3613334E-08 midg,1,midg; midg,igrid,midg -7.1201289E-09 1.1273876E-08 1,midg,midg; igrid,midg,midg 1.5488766E-08 -1.5813592E-08 gauss-seidel spectral radius is 0.9874866 estimated iterations to convergence 73 setup time was (sec) 0.5600000 now iterating at: 07:12:47 rms-change max change #iterations 0.1338595 21.51232 at 10iterations 1.3594720E-02 2.146101 at 20iterations 1.3191669E-03 0.2248173 at 30iterations 1.3357928E-04 2.2048950E-02 at 40iterations 1.3252908E-05 2.2430420E-03 at 50iterations finished qdiffx linear iterations at : 07:12:50 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 1.3252908E-05 2.2430420E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 07:12:51 4.006u 0.258s 0:04.51 94.2% 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 Sun Oct 9 2011 at 07:12:51 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: NAP 191 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.934467 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): -13.20100 38.48100 ymin,ymax (A): -22.20900 29.95500 zmin,zma (A): -15.64200 39.56700 x,y,z range (A): 51.68200 52.16400 55.20900 scale (grids/A): 1.934467 object centre (A): 12.64000 3.873000 11.96250 number of atom coordinates read : 2004 total number of charged atoms : 1867 net assigned charge : 1.000008 assigned positive charge : 299.9051 centred at (gu) : 91.58871 90.40141 87.74920 assigned negative charge : -298.9052 centred at (gu) : 92.04976 90.13335 87.32940 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 59434 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17860 grid for indexing accessible points = 1.400000 m= 21577 mr = 40170 m= 3218 mr = 15907 m= 159 mr = 1958 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1065 time to turn everything in is 0.5600000 number of dielectric boundary points 26287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 14712 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) : 0.6448224 object centre at (A) : 12.64000 3.873000 11.96250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4615859E-02 1.2150939E-02 midg,1,midg; midg,igrid,midg 1.2234758E-02 3.7191458E-02 1,midg,midg; igrid,midg,midg 1.0454252E-02 -2.8603660E-02 gauss-seidel spectral radius is 0.9986173 estimated iterations to convergence 213 setup time was (sec) 0.8500000 now iterating at: 07:12:52 rms-change max change #iterations 3.840764 176.2247 at 10iterations 1.787957 66.07973 at 20iterations 0.8291359 31.41085 at 30iterations 0.3877559 13.35481 at 40iterations 0.1797125 6.938707 at 50iterations 8.4120356E-02 3.196186 at 60iterations 3.9209574E-02 1.326294 at 70iterations 1.8201202E-02 0.6599493 at 80iterations 8.5179172E-03 0.3186131 at 90iterations 3.9522066E-03 0.1405058 at 100iterations 1.8430462E-03 6.8596840E-02 at 110iterations 8.5551629E-04 2.9479980E-02 at 120iterations finished qdiffx linear iterations at : 07:13:00 total time elapsed so far: 8.990000 # loops : 120 mean,max change (kT/e) : 8.5551629E-04 2.9479980E-02 energy calculations done at 8.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.160000 DelPhi exited at 07:13:01 9.165u 0.293s 0:09.71 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 Sun Oct 9 2011 at 07:13:01 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2004 !!! WARNING: NAP 191 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.901701 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): -13.20100 38.48100 ymin,ymax (A): -22.20900 29.95500 zmin,zma (A): -15.64200 39.56700 x,y,z range (A): 51.68200 52.16400 55.20900 scale (grids/A): 2.901701 object centre (A): 12.64000 3.873000 11.96250 number of atom coordinates read : 2004 total number of charged atoms : 1867 net assigned charge : 1.000008 assigned positive charge : 299.9051 centred at (gu) : 92.38309 90.60223 86.62387 assigned negative charge : -298.9052 centred at (gu) : 93.07475 90.20009 85.99391 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 137192 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17860 grid for indexing accessible points = 1.400000 m= 69215 mr = 97300 m= 24907 mr = 56593 m= 5685 mr = 19993 m= 728 mr = 4147 m= 47 mr = 489 m= 0 mr = 25 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 3814 time to turn everything in is 1.390000 number of dielectric boundary points 59227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 14931 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) : 1.934467 object centre at (A) : 12.64000 3.873000 11.96250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6266674 9.9408068E-02 midg,1,midg; midg,igrid,midg 0.1761223 0.4496776 1,midg,midg; igrid,midg,midg 0.1684912 -0.3087904 gauss-seidel spectral radius is 0.9992437 estimated iterations to convergence 287 setup time was (sec) 1.710000 now iterating at: 07:13:03 rms-change max change #iterations 8.815351 427.3744 at 10iterations 5.046196 114.2457 at 20iterations 2.884808 58.08244 at 30iterations 1.649584 32.16916 at 40iterations 0.9428442 20.17426 at 50iterations 0.5374337 12.09359 at 60iterations 0.3056632 5.841904 at 70iterations 0.1744555 3.183739 at 80iterations 9.9453472E-02 2.158264 at 90iterations 5.6660835E-02 1.152428 at 100iterations 3.2309040E-02 0.6553078 at 110iterations 1.8412651E-02 0.3672376 at 120iterations 1.0490544E-02 0.2058582 at 130iterations 5.9699551E-03 0.1282883 at 140iterations 3.4042576E-03 6.4368248E-02 at 150iterations 1.9386630E-03 3.6625385E-02 at 160iterations 1.1077522E-03 2.4267197E-02 at 170iterations 6.2966812E-04 1.1936188E-02 at 180iterations finished qdiffx linear iterations at : 07:13:16 total time elapsed so far: 15.68000 # loops : 180 mean,max change (kT/e) : 6.2966812E-04 1.1936188E-02 energy calculations done at 15.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.85000 DelPhi exited at 07:13:17 15.854u 0.306s 0:16.42 98.3% 0+0k 0+0io 0pf+0w