Tue Oct 11 06:01:29 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 06:01:29 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2268 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7348388 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): 25.60200 71.89600 ymin,ymax (A): -18.58900 29.85700 zmin,zma (A): 4.176000 46.23300 x,y,z range (A): 46.29400 48.44600 42.05700 scale (grids/A): 0.7348388 object centre (A): 48.74900 5.634001 25.20450 number of atom coordinates read : 2268 total number of charged atoms : 1949 net assigned charge : 6.500009 assigned positive charge : 315.1740 centred at (gu) : 89.24713 90.39893 90.20359 assigned negative charge : -308.6742 centred at (gu) : 89.37521 90.33844 90.28147 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7732 nv = 96 ne = 84 npr = 41308 no. pairs analyzed = 41308 no. exposed pairs = 2565 no. arc points = 17431 no. surface atoms = 879 nbur = 1389 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 591 mr = 4534 m= 5 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3669 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1525 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8218 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6324350E-07 3.3313420E-08 midg,1,midg; midg,igrid,midg 4.4716632E-08 1.6629487E-07 1,midg,midg; igrid,midg,midg 2.4532730E-07 -1.0315299E-08 gauss-seidel spectral radius is 0.9903407 estimated iterations to convergence 83 setup time was (sec) 0.5000000 now iterating at: 06:01:29 rms-change max change #iterations 0.2338540 37.45388 at 10iterations 3.1153571E-02 3.985984 at 20iterations 4.3756492E-03 0.5277033 at 30iterations 7.1373233E-04 8.9286804E-02 at 40iterations 1.7670683E-04 2.3775101E-02 at 50iterations finished qdiffx linear iterations at : 06:01:32 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 1.7670683E-04 2.3775101E-02 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 06:01:33 3.306u 0.167s 0:04.47 77.4% 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 06:01:33 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2268 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.204516 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): 25.60200 71.89600 ymin,ymax (A): -18.58900 29.85700 zmin,zma (A): 4.176000 46.23300 x,y,z range (A): 46.29400 48.44600 42.05700 scale (grids/A): 2.204516 object centre (A): 48.74900 5.634001 25.20450 number of atom coordinates read : 2268 total number of charged atoms : 1949 net assigned charge : 6.500009 assigned positive charge : 315.1740 centred at (gu) : 87.74146 91.19669 90.61067 assigned negative charge : -308.6742 centred at (gu) : 88.12589 91.01542 90.84456 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81508 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17431 grid for indexing accessible points = 1.400000 m= 34369 mr = 58503 m= 7386 mr = 26505 m= 791 mr = 5169 m= 27 mr = 407 m= 0 mr = 7 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 33490 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15502 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) : 0.7348388 object centre at (A) : 48.74900 5.634001 25.20450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5674103E-02 3.3897121E-02 midg,1,midg; midg,igrid,midg 5.4705322E-02 3.5675559E-02 1,midg,midg; igrid,midg,midg 4.7529191E-02 -5.6167435E-02 gauss-seidel spectral radius is 0.9989052 estimated iterations to convergence 239 setup time was (sec) 0.8900000 now iterating at: 06:01:34 rms-change max change #iterations 4.912290 183.5322 at 10iterations 2.484673 82.84439 at 20iterations 1.264773 37.26640 at 30iterations 0.6421296 18.22716 at 40iterations 0.3250309 9.255463 at 50iterations 0.1655177 4.548750 at 60iterations 8.4156297E-02 2.373962 at 70iterations 4.2784266E-02 1.137962 at 80iterations 2.1849791E-02 0.6229386 at 90iterations 1.1168223E-02 0.2942867 at 100iterations 5.7523008E-03 0.1791306 at 110iterations 2.9920209E-03 9.4951630E-02 at 120iterations finished qdiffx linear iterations at : 06:01:41 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 2.9920209E-03 9.4951630E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 06:01:42 7.680u 0.150s 0:08.27 94.6% 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 Tue Oct 11 2011 at 06:01:42 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2268 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: 3.306775 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): 25.60200 71.89600 ymin,ymax (A): -18.58900 29.85700 zmin,zma (A): 4.176000 46.23300 x,y,z range (A): 46.29400 48.44600 42.05700 scale (grids/A): 3.306775 object centre (A): 48.74900 5.634001 25.20450 number of atom coordinates read : 2268 total number of charged atoms : 1949 net assigned charge : 6.500009 assigned positive charge : 315.1740 centred at (gu) : 86.61226 91.79509 90.91595 assigned negative charge : -308.6742 centred at (gu) : 87.18887 91.52306 91.26676 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 187703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17431 grid for indexing accessible points = 1.400000 m= 104907 mr = 140478 m= 45199 mr = 88022 m= 14291 mr = 37769 m= 3164 mr = 11340 m= 428 mr = 2337 m= 27 mr = 305 m= 0 mr = 4 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.900000 number of dielectric boundary points 75464 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 15592 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) : 2.204516 object centre at (A) : 48.74900 5.634001 25.20450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1127720 0.2841343 midg,1,midg; midg,igrid,midg 0.3901195 0.1862118 1,midg,midg; igrid,midg,midg 0.4572609 -0.6719050 gauss-seidel spectral radius is 0.9993153 estimated iterations to convergence 301 setup time was (sec) 2.190000 now iterating at: 06:01:44 rms-change max change #iterations 10.69618 344.2867 at 10iterations 6.370658 123.9003 at 20iterations 3.790057 74.48076 at 30iterations 2.256861 41.57795 at 40iterations 1.337488 23.72624 at 50iterations 0.7914768 13.17373 at 60iterations 0.4681412 8.207157 at 70iterations 0.2770534 4.828514 at 80iterations 0.1635597 3.118698 at 90iterations 9.6663654E-02 1.632805 at 100iterations 5.7155255E-02 1.005703 at 110iterations 3.4006622E-02 0.5683327 at 120iterations 2.0263812E-02 0.3886471 at 130iterations 1.2248855E-02 0.2275076 at 140iterations 7.5746053E-03 0.1308670 at 150iterations 4.8727579E-03 9.1033936E-02 at 160iterations 3.2786664E-03 6.3163757E-02 at 170iterations 2.3518135E-03 4.0324211E-02 at 180iterations finished qdiffx linear iterations at : 06:01:53 total time elapsed so far: 11.48000 # loops : 180 mean,max change (kT/e) : 2.3518135E-03 4.0324211E-02 energy calculations done at 11.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.64000 DelPhi exited at 06:01:54 11.647u 0.184s 0:12.43 95.0% 0+0k 0+0io 0pf+0w