Sat Oct 8 15:48:41 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+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 15:48:41 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 has a net charge of -0.0940 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: 0.6479443 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): -2.211000 46.02900 ymin,ymax (A): -16.97100 29.56600 zmin,zma (A): -18.64100 36.30200 x,y,z range (A): 48.24000 46.53700 54.94300 scale (grids/A): 0.6479443 object centre (A): 21.90900 6.297500 8.830500 number of atom coordinates read : 2358 total number of charged atoms : 2295 net assigned charge : 2.806005 assigned positive charge : 354.2439 centred at (gu) : 90.85902 88.93617 90.20454 assigned negative charge : -351.4387 centred at (gu) : 90.92591 89.05493 90.25891 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6775 nv = 96 ne = 84 npr = 46825 no. pairs analyzed = 46825 no. exposed pairs = 2999 no. arc points = 20652 no. surface atoms = 1024 nbur = 1334 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 363 mr = 3765 m= 0 mr = 49 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2031 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8130 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1589465E-08 -2.2130715E-09 midg,1,midg; midg,igrid,midg 2.5564006E-08 -8.4424805E-09 1,midg,midg; igrid,midg,midg 1.1446355E-08 -4.5968300E-09 gauss-seidel spectral radius is 0.9876389 estimated iterations to convergence 73 setup time was (sec) 0.6200000 now iterating at: 15:48:42 rms-change max change #iterations 0.1485500 30.48116 at 10iterations 1.5119059E-02 2.130344 at 20iterations 1.5541420E-03 0.2034454 at 30iterations 1.8105317E-04 2.4847984E-02 at 40iterations 2.9321729E-05 4.3258667E-03 at 50iterations finished qdiffx linear iterations at : 15:48:46 total time elapsed so far: 5.090000 # loops : 50 mean,max change (kT/e) : 2.9321729E-05 4.3258667E-03 energy calculations done at 5.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.260000 DelPhi exited at 15:48:47 5.261u 0.454s 0:06.01 95.0% 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 15:48:47 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 = 2358 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 has a net charge of -0.0940 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: 1.943833 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): -2.211000 46.02900 ymin,ymax (A): -16.97100 29.56600 zmin,zma (A): -18.64100 36.30200 x,y,z range (A): 48.24000 46.53700 54.94300 scale (grids/A): 1.943833 object centre (A): 21.90900 6.297500 8.830500 number of atom coordinates read : 2358 total number of charged atoms : 2295 net assigned charge : 2.806005 assigned positive charge : 354.2439 centred at (gu) : 92.57662 86.80817 90.61305 assigned negative charge : -351.4387 centred at (gu) : 92.77766 87.16488 90.77660 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73195 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20652 grid for indexing accessible points = 1.400000 m= 26598 mr = 51196 m= 4448 mr = 19632 m= 257 mr = 2910 m= 3 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 797 time to turn everything in is 0.6300000 number of dielectric boundary points 30692 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 18124 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) : 0.6479443 object centre at (A) : 21.90900 6.297500 8.830500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9988630E-02 7.7785673E-03 midg,1,midg; midg,igrid,midg 1.9776588E-02 -6.8646236E-03 1,midg,midg; igrid,midg,midg 6.4535630E-03 -4.8031893E-02 gauss-seidel spectral radius is 0.9986680 estimated iterations to convergence 217 setup time was (sec) 0.9900000 now iterating at: 15:48:48 rms-change max change #iterations 4.214159 180.9928 at 10iterations 1.986810 100.9613 at 20iterations 0.9397402 32.06200 at 30iterations 0.4456036 15.73856 at 40iterations 0.2109538 6.712219 at 50iterations 9.9929266E-02 3.180178 at 60iterations 4.7287971E-02 1.414962 at 70iterations 2.2421960E-02 0.7186931 at 80iterations 1.0634788E-02 0.3402863 at 90iterations 5.0369343E-03 0.1612415 at 100iterations 2.3892706E-03 7.5351954E-02 at 110iterations 1.1376735E-03 3.4690857E-02 at 120iterations finished qdiffx linear iterations at : 15:49:00 total time elapsed so far: 12.57000 # loops : 120 mean,max change (kT/e) : 1.1376735E-03 3.4690857E-02 energy calculations done at 12.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 15:49:00 12.757u 0.504s 0:13.53 97.9% 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 15:49:01 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 = 2358 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 has a net charge of -0.0940 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: 2.915749 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): -2.211000 46.02900 ymin,ymax (A): -16.97100 29.56600 zmin,zma (A): -18.64100 36.30200 x,y,z range (A): 48.24000 46.53700 54.94300 scale (grids/A): 2.915749 object centre (A): 21.90900 6.297500 8.830500 number of atom coordinates read : 2358 total number of charged atoms : 2295 net assigned charge : 2.806005 assigned positive charge : 354.2439 centred at (gu) : 93.86485 85.21210 90.91940 assigned negative charge : -351.4387 centred at (gu) : 94.16644 85.74724 91.16483 start vw surface at 0.1100000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 169409 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20652 grid for indexing accessible points = 1.400000 m= 85446 mr = 124042 m= 31910 mr = 70056 m= 8317 mr = 25902 m= 1147 mr = 6326 m= 48 mr = 738 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 2580 time to turn everything in is 1.650000 number of dielectric boundary points 69207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 18356 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) : 1.943833 object centre at (A) : 21.90900 6.297500 8.830500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3421704 7.5883590E-02 midg,1,midg; midg,igrid,midg 0.1245060 -0.1109566 1,midg,midg; igrid,midg,midg 7.5575694E-02 -0.6229318 gauss-seidel spectral radius is 0.9992681 estimated iterations to convergence 292 setup time was (sec) 2.060000 now iterating at: 15:49:03 rms-change max change #iterations 9.837659 509.7643 at 10iterations 5.784418 145.3435 at 20iterations 3.384602 75.71910 at 30iterations 1.979987 48.04136 at 40iterations 1.153605 23.15602 at 50iterations 0.6711472 12.98980 at 60iterations 0.3889568 7.499691 at 70iterations 0.2253312 4.245458 at 80iterations 0.1308955 2.324387 at 90iterations 7.5690918E-02 1.396300 at 100iterations 4.3672442E-02 0.8568659 at 110iterations 2.5267167E-02 0.4601316 at 120iterations 1.4610358E-02 0.2864456 at 130iterations 8.4195565E-03 0.1535187 at 140iterations 4.8586824E-03 8.1275940E-02 at 150iterations 2.8005040E-03 5.1520586E-02 at 160iterations 1.6187865E-03 2.7773857E-02 at 170iterations 9.3491259E-04 1.6125679E-02 at 180iterations finished qdiffx linear iterations at : 15:49:24 total time elapsed so far: 23.27000 # loops : 180 mean,max change (kT/e) : 9.3491259E-04 1.6125679E-02 energy calculations done at 23.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.44000 DelPhi exited at 15:49:25 23.442u 0.540s 0:24.34 98.5% 0+0k 0+0io 0pf+0w