Mon Oct 10 14:00:15 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 Mon Oct 10 2011 at 14:00:16 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1688 !!! WARNING: NAP 164 has a net charge of -2.7230 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: 0.7346871 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): 4.115000 48.37000 ymin,ymax (A): 21.55400 70.01000 zmin,zma (A): -8.477000 35.91800 x,y,z range (A): 44.25500 48.45600 44.39500 scale (grids/A): 0.7346871 object centre (A): 26.24250 45.78200 13.72050 number of atom coordinates read : 1688 total number of charged atoms : 1551 net assigned charge : -12.22299 assigned positive charge : 249.5312 centred at (gu) : 90.77444 89.39938 89.56890 assigned negative charge : -261.7541 centred at (gu) : 90.79786 89.22010 89.94724 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6183 nv = 96 ne = 84 npr = 36594 no. pairs analyzed = 36594 no. exposed pairs = 2074 no. arc points = 14837 no. surface atoms = 700 nbur = 988 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 3475 m= 2 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 165 time to turn everything in is 0.2400000 number of dielectric boundary points 3048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1146 ## 78 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6550 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8304958E-08 -4.4578317E-07 midg,1,midg; midg,igrid,midg -3.6597694E-07 -5.4764456E-08 1,midg,midg; igrid,midg,midg -1.5135485E-07 -2.4058286E-07 gauss-seidel spectral radius is 0.9903030 estimated iterations to convergence 83 setup time was (sec) 0.4500000 now iterating at: 14:00:16 rms-change max change #iterations 0.2184807 32.65307 at 10iterations 2.9038753E-02 3.966484 at 20iterations 3.8323994E-03 0.5099068 at 30iterations 4.9778417E-04 6.3220978E-02 at 40iterations 6.6679153E-05 8.3112717E-03 at 50iterations finished qdiffx linear iterations at : 14:00:19 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 6.6679153E-05 8.3112717E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.070000 DelPhi exited at 14:00:20 3.070u 0.139s 0:04.68 68.3% 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 Mon Oct 10 2011 at 14:00:20 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1688 !!! WARNING: NAP 164 has a net charge of -2.7230 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: 2.204061 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): 4.115000 48.37000 ymin,ymax (A): 21.55400 70.01000 zmin,zma (A): -8.477000 35.91800 x,y,z range (A): 44.25500 48.45600 44.39500 scale (grids/A): 2.204061 object centre (A): 26.24250 45.78200 13.72050 number of atom coordinates read : 1688 total number of charged atoms : 1551 net assigned charge : -12.22299 assigned positive charge : 249.5312 centred at (gu) : 92.32358 88.19832 88.70684 assigned negative charge : -261.7541 centred at (gu) : 92.39356 87.66035 89.84163 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 64551 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14837 grid for indexing accessible points = 1.400000 m= 26203 mr = 44299 m= 5386 mr = 20233 m= 503 mr = 3796 m= 15 mr = 280 m= 0 mr = 5 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 4212 time to turn everything in is 0.4800000 number of dielectric boundary points 28045 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 12352 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) : 0.7346871 object centre at (A) : 26.24250 45.78200 13.72050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8807970E-02 -9.7056761E-02 midg,1,midg; midg,igrid,midg -9.2906728E-02 -2.9723870E-03 1,midg,midg; igrid,midg,midg -5.9490953E-02 -7.6528892E-02 gauss-seidel spectral radius is 0.9988706 estimated iterations to convergence 235 setup time was (sec) 0.7500000 now iterating at: 14:00:21 rms-change max change #iterations 4.527242 198.8236 at 10iterations 2.273739 79.94802 at 20iterations 1.139215 41.11855 at 30iterations 0.5685734 19.39120 at 40iterations 0.2850870 9.459631 at 50iterations 0.1432718 4.587936 at 60iterations 7.1642756E-02 2.543391 at 70iterations 3.5716478E-02 1.055962 at 80iterations 1.7981691E-02 0.5903301 at 90iterations 9.0123052E-03 0.2916002 at 100iterations 4.5277565E-03 0.1642914 at 110iterations 2.2706222E-03 7.5813293E-02 at 120iterations finished qdiffx linear iterations at : 14:00:27 total time elapsed so far: 6.750000 # loops : 120 mean,max change (kT/e) : 2.2706222E-03 7.5813293E-02 energy calculations done at 6.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.930000 DelPhi exited at 14:00:29 6.932u 0.176s 0:08.59 82.6% 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 Mon Oct 10 2011 at 14:00:29 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1688 !!! WARNING: NAP 164 has a net charge of -2.7230 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: 3.306092 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): 4.115000 48.37000 ymin,ymax (A): 21.55400 70.01000 zmin,zma (A): -8.477000 35.91800 x,y,z range (A): 44.25500 48.45600 44.39500 scale (grids/A): 3.306092 object centre (A): 26.24250 45.78200 13.72050 number of atom coordinates read : 1688 total number of charged atoms : 1551 net assigned charge : -12.22299 assigned positive charge : 249.5312 centred at (gu) : 93.48534 87.29758 88.06035 assigned negative charge : -261.7541 centred at (gu) : 93.59027 86.49062 89.76254 start vw surface at 0.1300000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 148453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14837 grid for indexing accessible points = 1.400000 m= 79747 mr = 106671 m= 34488 mr = 66483 m= 10365 mr = 29079 m= 2084 mr = 8223 m= 264 mr = 1621 m= 20 mr = 182 m= 0 mr = 10 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 14146 time to turn everything in is 1.520000 number of dielectric boundary points 63152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 12408 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) : 2.204061 object centre at (A) : 26.24250 45.78200 13.72050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4351557 -0.6885868 midg,1,midg; midg,igrid,midg -0.7643025 4.9696159E-02 1,midg,midg; igrid,midg,midg -0.3994405 -0.5882769 gauss-seidel spectral radius is 0.9992982 estimated iterations to convergence 298 setup time was (sec) 1.810000 now iterating at: 14:00:31 rms-change max change #iterations 9.844145 372.1544 at 10iterations 5.740072 126.6842 at 20iterations 3.335552 69.68128 at 30iterations 1.941473 35.13357 at 40iterations 1.128779 20.30296 at 50iterations 0.6578583 12.03776 at 60iterations 0.3826638 7.420664 at 70iterations 0.2227367 4.065612 at 80iterations 0.1294346 2.695583 at 90iterations 7.5417176E-02 1.303504 at 100iterations 4.3822158E-02 0.7707233 at 110iterations 2.5499312E-02 0.4370556 at 120iterations 1.4851307E-02 0.2807922 at 130iterations 8.6227264E-03 0.1667147 at 140iterations 5.0213165E-03 8.8851213E-02 at 150iterations 2.9239783E-03 5.1515579E-02 at 160iterations 1.7041070E-03 3.2073021E-02 at 170iterations 9.9251361E-04 1.7989635E-02 at 180iterations finished qdiffx linear iterations at : 14:00:41 total time elapsed so far: 11.72000 # loops : 180 mean,max change (kT/e) : 9.9251361E-04 1.7989635E-02 energy calculations done at 11.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.89000 DelPhi exited at 14:00:41 11.897u 0.217s 0:12.44 97.2% 0+0k 0+0io 0pf+0w