Tue Oct 11 08:22:04 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+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 Oct 11 2011 at 08:22:04 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 = 3382 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5699556 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): 59.66100 111.2680 ymin,ymax (A): 26.61800 89.07900 zmin,zma (A): 25.40500 86.38100 x,y,z range (A): 51.60700 62.46100 60.97600 scale (grids/A): 0.5699556 object centre (A): 85.46450 57.84850 55.89300 number of atom coordinates read : 3382 total number of charged atoms : 3232 net assigned charge : 6.500038 assigned positive charge : 519.8464 centred at (gu) : 87.76900 91.16659 91.41165 assigned negative charge : -513.3479 centred at (gu) : 87.81233 91.13776 91.56505 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7708 nv = 96 ne = 84 npr = 62974 no. pairs analyzed = 62974 no. exposed pairs = 4867 no. arc points = 34515 no. surface atoms = 1630 nbur = 1752 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 375 mr = 3742 m= 0 mr = 35 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 4306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3571 ## 422 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9643 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6520455E-09 -2.5605011E-09 midg,1,midg; midg,igrid,midg 3.7780198E-10 2.0026512E-09 1,midg,midg; igrid,midg,midg 3.0294665E-09 1.4683531E-10 gauss-seidel spectral radius is 0.9841686 estimated iterations to convergence 65 setup time was (sec) 0.4300000 now iterating at: 08:22:05 rms-change max change #iterations 9.8719597E-02 15.45110 at 10iterations 7.3461654E-03 1.189111 at 20iterations 6.1618211E-04 8.8541031E-02 at 30iterations 1.0067356E-04 1.4645576E-02 at 40iterations 2.9610626E-05 3.8952827E-03 at 50iterations finished qdiffx linear iterations at : 08:22:08 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 2.9610626E-05 3.8952827E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 08:22:08 3.479u 0.170s 0:04.16 87.5% 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 Oct 11 2011 at 08:22:08 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 = 3382 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.709867 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): 59.66100 111.2680 ymin,ymax (A): 26.61800 89.07900 zmin,zma (A): 25.40500 86.38100 x,y,z range (A): 51.60700 62.46100 60.97600 scale (grids/A): 1.709867 object centre (A): 85.46450 57.84850 55.89300 number of atom coordinates read : 3382 total number of charged atoms : 3232 net assigned charge : 6.500038 assigned positive charge : 519.8464 centred at (gu) : 83.30622 93.49854 94.23399 assigned negative charge : -513.3479 centred at (gu) : 83.43683 93.41277 94.69468 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84184 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34515 grid for indexing accessible points = 1.400000 m= 28435 mr = 55474 m= 3706 mr = 19068 m= 151 mr = 1850 m= 1 mr = 25 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 0.4100000 number of dielectric boundary points 40060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 355 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 25021 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) : 0.5699556 object centre at (A) : 85.46450 57.84850 55.89300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8022841E-03 -2.7356662E-02 midg,1,midg; midg,igrid,midg 2.2047438E-02 3.9588116E-02 1,midg,midg; igrid,midg,midg 2.0490918E-02 1.0398966E-03 gauss-seidel spectral radius is 0.9984129 estimated iterations to convergence 199 setup time was (sec) 0.6400000 now iterating at: 08:22:09 rms-change max change #iterations 4.006792 172.6617 at 10iterations 1.753505 67.07568 at 20iterations 0.7705598 25.58311 at 30iterations 0.3386342 10.75147 at 40iterations 0.1494617 5.117176 at 50iterations 6.5507248E-02 2.150346 at 60iterations 2.9009981E-02 0.9621639 at 70iterations 1.2778665E-02 0.4125500 at 80iterations 5.6215404E-03 0.2044678 at 90iterations 2.5000144E-03 8.4948599E-02 at 100iterations 1.1054341E-03 3.7723064E-02 at 110iterations 4.9401727E-04 1.5500069E-02 at 120iterations finished qdiffx linear iterations at : 08:22:16 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 4.9401727E-04 1.5500069E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 08:22:17 7.910u 0.212s 0:08.42 96.4% 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 Tue Oct 11 2011 at 08:22:17 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 = 3382 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.564800 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): 59.66100 111.2680 ymin,ymax (A): 26.61800 89.07900 zmin,zma (A): 25.40500 86.38100 x,y,z range (A): 51.60700 62.46100 60.97600 scale (grids/A): 2.564800 object centre (A): 85.46450 57.84850 55.89300 number of atom coordinates read : 3382 total number of charged atoms : 3232 net assigned charge : 6.500038 assigned positive charge : 519.8464 centred at (gu) : 79.95921 95.24749 96.35073 assigned negative charge : -513.3479 centred at (gu) : 80.15510 95.11899 97.04201 start vw surface at 0.1100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 194863 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34515 grid for indexing accessible points = 1.400000 m= 94308 mr = 135953 m= 30453 mr = 73134 m= 6033 mr = 22542 m= 578 mr = 3916 m= 26 mr = 260 m= 0 mr = 6 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.040000 number of dielectric boundary points 90450 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 25847 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) : 1.709867 object centre at (A) : 85.46450 57.84850 55.89300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.7294717E-02 -0.1946170 midg,1,midg; midg,igrid,midg 0.2894400 0.5584894 1,midg,midg; igrid,midg,midg 0.3206880 3.8849032E-03 gauss-seidel spectral radius is 0.9992238 estimated iterations to convergence 283 setup time was (sec) 1.280000 now iterating at: 08:22:18 rms-change max change #iterations 10.09428 326.0305 at 10iterations 5.924512 144.6373 at 20iterations 3.439719 66.54743 at 30iterations 1.989935 47.61803 at 40iterations 1.145050 24.73886 at 50iterations 0.6567870 12.62945 at 60iterations 0.3751817 7.755414 at 70iterations 0.2144580 4.434303 at 80iterations 0.1223823 2.835390 at 90iterations 6.9689021E-02 1.415185 at 100iterations 3.9679758E-02 0.8502655 at 110iterations 2.2536773E-02 0.4498034 at 120iterations 1.2809940E-02 0.2444725 at 130iterations 7.2779539E-03 0.1503448 at 140iterations 4.1352878E-03 7.3421478E-02 at 150iterations 2.3422001E-03 4.1412354E-02 at 160iterations 1.3295660E-03 2.4282455E-02 at 170iterations 7.5588055E-04 1.4656305E-02 at 180iterations finished qdiffx linear iterations at : 08:22:30 total time elapsed so far: 13.06000 # loops : 180 mean,max change (kT/e) : 7.5588055E-04 1.4656305E-02 energy calculations done at 13.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 08:22:31 13.186u 0.242s 0:13.83 97.0% 0+0k 0+0io 0pf+0w