Tue Oct 11 08:06:04 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+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 Tue Oct 11 2011 at 08:06:04 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3100 !!! WARNING: HIR 154 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5466158 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): -20.89400 42.93000 ymin,ymax (A): -1.877000 63.25100 zmin,zma (A): 7.061000 55.66100 x,y,z range (A): 63.82400 65.12801 48.60000 scale (grids/A): 0.5466158 object centre (A): 11.01800 30.68700 31.36100 number of atom coordinates read : 3100 total number of charged atoms : 2953 net assigned charge : 9.514022 assigned positive charge : 465.1577 centred at (gu) : 89.89264 90.87332 89.58650 assigned negative charge : -455.6450 centred at (gu) : 89.78313 90.91511 89.62768 start vw surface at 0.2100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 6207 nv = 96 ne = 84 npr = 58214 no. pairs analyzed = 58214 no. exposed pairs = 4389 no. arc points = 31738 no. surface atoms = 1472 nbur = 1628 mkacc time = 0.1300000 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 = 1.568000 m= 251 mr = 2894 m= 0 mr = 3 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.3600000 number of dielectric boundary points 3561 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3154 ## 418 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9078834E-10 2.9242023E-10 midg,1,midg; midg,igrid,midg 7.2816464E-10 3.8769929E-10 1,midg,midg; igrid,midg,midg -1.6944962E-10 1.3275945E-09 gauss-seidel spectral radius is 0.9827717 estimated iterations to convergence 63 setup time was (sec) 0.5800000 now iterating at: 08:06:05 rms-change max change #iterations 7.4351974E-02 13.45528 at 10iterations 4.9406406E-03 0.7164450 at 20iterations 3.3145869E-04 5.0184250E-02 at 30iterations 2.3347277E-05 4.2897463E-03 at 40iterations 1.7746631E-06 2.6893616E-04 at 50iterations finished qdiffx linear iterations at : 08:06:07 total time elapsed so far: 3.010000 # loops : 50 mean,max change (kT/e) : 1.7746631E-06 2.6893616E-04 energy calculations done at 3.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 08:06:08 3.175u 0.138s 0:03.91 84.3% 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 Tue Oct 11 2011 at 08:06:08 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3100 !!! WARNING: HIR 154 has a net charge of 0.5140 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: 1.639848 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): -20.89400 42.93000 ymin,ymax (A): -1.877000 63.25100 zmin,zma (A): 7.061000 55.66100 x,y,z range (A): 63.82400 65.12801 48.60000 scale (grids/A): 1.639848 object centre (A): 11.01800 30.68700 31.36100 number of atom coordinates read : 3100 total number of charged atoms : 2953 net assigned charge : 9.514022 assigned positive charge : 465.1577 centred at (gu) : 89.67681 92.61890 88.75838 assigned negative charge : -455.6450 centred at (gu) : 89.34893 92.74474 88.88285 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 68203 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31738 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19810 mr = 42940 m= 1921 mr = 13047 m= 50 mr = 843 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 381 time to turn everything in is 0.4800000 number of dielectric boundary points 33152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 370 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 22645 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) : 0.5466158 object centre at (A) : 11.01800 30.68700 31.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.0116447E-03 6.5704742E-03 midg,1,midg; midg,igrid,midg -4.7820997E-03 -1.1056550E-02 1,midg,midg; igrid,midg,midg 1.1416337E-03 2.3173038E-02 gauss-seidel spectral radius is 0.9982302 estimated iterations to convergence 189 setup time was (sec) 0.7400000 now iterating at: 08:06:09 rms-change max change #iterations 3.416748 152.5649 at 10iterations 1.426646 53.64297 at 20iterations 0.5965416 22.94404 at 30iterations 0.2513873 9.683064 at 40iterations 0.1058661 3.889320 at 50iterations 4.4301350E-02 1.566181 at 60iterations 1.8641528E-02 0.6618376 at 70iterations 7.8459475E-03 0.2785158 at 80iterations 3.2995618E-03 0.1275473 at 90iterations 1.3863744E-03 4.8654556E-02 at 100iterations 5.8383914E-04 2.0139456E-02 at 110iterations 2.4448920E-04 8.8348389E-03 at 120iterations finished qdiffx linear iterations at : 08:06:15 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 2.4448920E-04 8.8348389E-03 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 08:06:15 7.064u 0.169s 0:07.69 93.8% 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 08:06:16 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3100 !!! WARNING: HIR 154 has a net charge of 0.5140 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: 2.459771 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): -20.89400 42.93000 ymin,ymax (A): -1.877000 63.25100 zmin,zma (A): 7.061000 55.66100 x,y,z range (A): 63.82400 65.12801 48.60000 scale (grids/A): 2.459771 object centre (A): 11.01800 30.68700 31.36100 number of atom coordinates read : 3100 total number of charged atoms : 2953 net assigned charge : 9.514022 assigned positive charge : 465.1577 centred at (gu) : 89.51502 93.92804 88.13741 assigned negative charge : -455.6450 centred at (gu) : 89.02342 94.11703 88.32407 start vw surface at 0.1500000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 158568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31738 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 68633 mr = 106264 m= 19059 mr = 52380 m= 2858 mr = 13948 m= 197 mr = 1786 m= 3 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 1290 time to turn everything in is 1.120000 number of dielectric boundary points 74869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 23601 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) : 1.639848 object centre at (A) : 11.01800 30.68700 31.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1120899E-02 9.1396928E-02 midg,1,midg; midg,igrid,midg -0.1058797 -6.4627163E-02 1,midg,midg; igrid,midg,midg 2.8262649E-02 0.3059812 gauss-seidel spectral radius is 0.9991629 estimated iterations to convergence 273 setup time was (sec) 1.410000 now iterating at: 08:06:17 rms-change max change #iterations 8.944471 282.1917 at 10iterations 5.090576 127.6353 at 20iterations 2.885475 88.46577 at 30iterations 1.623551 37.56300 at 40iterations 0.9092744 25.22829 at 50iterations 0.5079577 10.54357 at 60iterations 0.2826650 6.219597 at 70iterations 0.1576001 3.239284 at 80iterations 8.7381385E-02 1.855244 at 90iterations 4.8476372E-02 0.9767838 at 100iterations 2.6960328E-02 0.5329282 at 110iterations 1.4870737E-02 0.2870369 at 120iterations 8.2791373E-03 0.1662774 at 130iterations 4.5885839E-03 8.9736938E-02 at 140iterations 2.5373125E-03 5.3091049E-02 at 150iterations 1.4056754E-03 2.9611588E-02 at 160iterations 7.7995565E-04 1.5569687E-02 at 170iterations 4.3081975E-04 8.3885193E-03 at 180iterations finished qdiffx linear iterations at : 08:06:28 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 4.3081975E-04 8.3885193E-03 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.05000 DelPhi exited at 08:06:28 12.054u 0.210s 0:12.86 95.3% 0+0k 0+0io 0pf+0w