Sat Oct 8 22:16:41 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 Sat Oct 8 2011 at 22:16:41 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 = 2263 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6566085 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): -15.39900 27.94000 ymin,ymax (A): -11.48600 41.89700 zmin,zma (A): 0.1090001 54.32700 x,y,z range (A): 43.33900 53.38300 54.21800 scale (grids/A): 0.6566085 object centre (A): 6.270501 15.20550 27.21800 number of atom coordinates read : 2263 total number of charged atoms : 2129 net assigned charge : 11.00003 assigned positive charge : 328.6806 centred at (gu) : 88.45735 91.25482 89.35974 assigned negative charge : -317.6813 centred at (gu) : 88.57524 91.25939 89.37343 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6799 nv = 96 ne = 84 npr = 45057 no. pairs analyzed = 45057 no. exposed pairs = 3000 no. arc points = 20903 no. surface atoms = 1008 nbur = 1255 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 455 mr = 3664 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2002 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7814 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0874325E-08 2.0298099E-08 midg,1,midg; midg,igrid,midg 2.0042178E-08 3.1480077E-08 1,midg,midg; igrid,midg,midg 5.8315965E-08 5.7088791E-09 gauss-seidel spectral radius is 0.9879566 estimated iterations to convergence 74 setup time was (sec) 0.5200000 now iterating at: 22:16:42 rms-change max change #iterations 0.1471518 24.38092 at 10iterations 1.5464111E-02 2.253613 at 20iterations 1.6571785E-03 0.2577150 at 30iterations 1.9823120E-04 3.2684326E-02 at 40iterations 2.9510982E-05 4.0111542E-03 at 50iterations finished qdiffx linear iterations at : 22:16:44 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 2.9510982E-05 4.0111542E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 22:16:45 3.131u 0.131s 0:03.54 92.0% 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 22:16:45 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 = 2263 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: 1.969826 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): -15.39900 27.94000 ymin,ymax (A): -11.48600 41.89700 zmin,zma (A): 0.1090001 54.32700 x,y,z range (A): 43.33900 53.38300 54.21800 scale (grids/A): 1.969826 object centre (A): 6.270501 15.20550 27.21800 number of atom coordinates read : 2263 total number of charged atoms : 2129 net assigned charge : 11.00003 assigned positive charge : 328.6806 centred at (gu) : 85.37168 93.76442 88.07915 assigned negative charge : -317.6813 centred at (gu) : 85.72578 93.77843 88.12046 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 72083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20903 grid for indexing accessible points = 1.400000 m= 27392 mr = 48842 m= 5255 mr = 19892 m= 385 mr = 3419 m= 7 mr = 157 m= 0 mr = 3 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 32809 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 136 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 16800 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) : 0.6566085 object centre at (A) : 6.270501 15.20550 27.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0261745E-02 4.4950861E-02 midg,1,midg; midg,igrid,midg 6.2451858E-02 3.0433474E-02 1,midg,midg; igrid,midg,midg 3.8044967E-02 -4.6675205E-03 gauss-seidel spectral radius is 0.9986919 estimated iterations to convergence 219 setup time was (sec) 0.7700000 now iterating at: 22:16:46 rms-change max change #iterations 4.061280 214.4003 at 10iterations 1.934340 67.08235 at 20iterations 0.9177012 30.00739 at 30iterations 0.4358278 16.47279 at 40iterations 0.2078512 6.556221 at 50iterations 9.8752379E-02 3.278786 at 60iterations 4.6919052E-02 1.474522 at 70iterations 2.2323800E-02 0.7330093 at 80iterations 1.0651062E-02 0.3628855 at 90iterations 5.0660791E-03 0.1787720 at 100iterations 2.4142028E-03 7.6416016E-02 at 110iterations 1.1542713E-03 3.8330078E-02 at 120iterations finished qdiffx linear iterations at : 22:16:52 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 1.1542713E-03 3.8330078E-02 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.980000 DelPhi exited at 22:16:52 6.981u 0.158s 0:07.45 95.7% 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 22:16:52 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 = 2263 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: 2.954738 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): -15.39900 27.94000 ymin,ymax (A): -11.48600 41.89700 zmin,zma (A): 0.1090001 54.32700 x,y,z range (A): 43.33900 53.38300 54.21800 scale (grids/A): 2.954738 object centre (A): 6.270501 15.20550 27.21800 number of atom coordinates read : 2263 total number of charged atoms : 2129 net assigned charge : 11.00003 assigned positive charge : 328.6806 centred at (gu) : 83.05759 95.64645 87.11871 assigned negative charge : -317.6813 centred at (gu) : 83.58871 95.66759 87.18073 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 166421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20903 grid for indexing accessible points = 1.400000 m= 85803 mr = 118763 m= 34281 mr = 69380 m= 9778 mr = 27282 m= 1695 mr = 7426 m= 129 mr = 1145 m= 7 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.300000 number of dielectric boundary points 74048 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 17032 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) : 1.969826 object centre at (A) : 6.270501 15.20550 27.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5806786 0.5209476 midg,1,midg; midg,igrid,midg 0.7607401 0.3136075 1,midg,midg; igrid,midg,midg 0.3421336 -4.2789418E-02 gauss-seidel spectral radius is 0.9992805 estimated iterations to convergence 294 setup time was (sec) 1.580000 now iterating at: 22:16:54 rms-change max change #iterations 9.623176 379.5965 at 10iterations 5.718702 132.0246 at 20iterations 3.389922 89.36211 at 30iterations 1.999919 41.45708 at 40iterations 1.172598 23.76506 at 50iterations 0.6884216 13.47833 at 60iterations 0.4025196 7.781967 at 70iterations 0.2343887 4.720036 at 80iterations 0.1368508 2.565372 at 90iterations 7.9562597E-02 1.449165 at 100iterations 4.6274807E-02 0.8658180 at 110iterations 2.6900012E-02 0.5213690 at 120iterations 1.5642209E-02 0.2768211 at 130iterations 9.0754079E-03 0.1611547 at 140iterations 5.2654757E-03 9.8112106E-02 at 150iterations 3.0600231E-03 5.4298401E-02 at 160iterations 1.7782875E-03 3.1759262E-02 at 170iterations 1.0357163E-03 1.8417358E-02 at 180iterations finished qdiffx linear iterations at : 22:17:04 total time elapsed so far: 11.04000 # loops : 180 mean,max change (kT/e) : 1.0357163E-03 1.8417358E-02 energy calculations done at 11.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.24000 DelPhi exited at 22:17:04 11.243u 0.175s 0:11.70 97.5% 0+0k 0+0io 0pf+0w