Sun Feb 12 01:10:54 PST 2012 #!/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 Sun Feb 12 2012 at 01:10:56 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2555 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: 0.5726050 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): -11.81200 37.17300 ymin,ymax (A): -28.34400 22.17900 zmin,zma (A): 31.73700 93.90900 x,y,z range (A): 48.98500 50.52300 62.17200 scale (grids/A): 0.5726050 object centre (A): 12.68050 -3.082500 62.82300 number of atom coordinates read : 2555 total number of charged atoms : 2339 net assigned charge : -7.999981 assigned positive charge : 329.3683 centred at (gu) : 91.45456 88.19672 91.07822 assigned negative charge : -337.3690 centred at (gu) : 91.38847 88.24052 91.34323 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5478 nv = 96 ne = 84 npr = 58367 no. pairs analyzed = 58367 no. exposed pairs = 3524 no. arc points = 24849 no. surface atoms = 1187 nbur = 1368 mkacc time = 0.1100000 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 = 1.512000 m= 272 mr = 2499 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2272 ## 166 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6793 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5353750E-09 -6.2853758E-09 midg,1,midg; midg,igrid,midg -1.1231100E-09 -1.2441002E-09 1,midg,midg; igrid,midg,midg -1.5533101E-09 -6.3383898E-10 gauss-seidel spectral radius is 0.9842377 estimated iterations to convergence 65 setup time was (sec) 0.4400000 now iterating at: 01:10:57 rms-change max change #iterations 7.6860264E-02 14.09747 at 10iterations 6.3204649E-03 1.005341 at 20iterations 7.9460460E-04 0.1324806 at 30iterations 1.9286598E-04 3.0179977E-02 at 40iterations 5.5175271E-05 8.6364746E-03 at 50iterations finished qdiffx linear iterations at : 01:11:00 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 5.5175271E-05 8.6364746E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 01:11:00 3.540u 0.181s 0:04.03 92.3% 0+0k 0+45840io 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 Sun Feb 12 2012 at 01:11:00 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2555 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: 1.717815 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): -11.81200 37.17300 ymin,ymax (A): -28.34400 22.17900 zmin,zma (A): 31.73700 93.90900 x,y,z range (A): 48.98500 50.52300 62.17200 scale (grids/A): 1.717815 object centre (A): 12.68050 -3.082500 62.82300 number of atom coordinates read : 2555 total number of charged atoms : 2339 net assigned charge : -7.999981 assigned positive charge : 329.3683 centred at (gu) : 94.36314 84.59005 93.23455 assigned negative charge : -337.3690 centred at (gu) : 94.16523 84.72153 94.02958 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 59831 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24849 grid for indexing accessible points = 1.400000 m= 18239 mr = 37876 m= 2251 mr = 11457 m= 79 mr = 991 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 174 time to turn everything in is 0.3900000 number of dielectric boundary points 30070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 100 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 18181 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) : 0.5726050 object centre at (A) : 12.68050 -3.082500 62.82300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3291213E-02 -4.7911193E-02 midg,1,midg; midg,igrid,midg -5.0869037E-04 -3.2661848E-03 1,midg,midg; igrid,midg,midg -6.7763566E-03 -3.6883333E-03 gauss-seidel spectral radius is 0.9983404 estimated iterations to convergence 195 setup time was (sec) 0.6100000 now iterating at: 01:11:01 rms-change max change #iterations 3.182087 163.3735 at 10iterations 1.370698 53.14640 at 20iterations 0.5902139 22.85970 at 30iterations 0.2564003 9.946136 at 40iterations 0.1110659 4.473267 at 50iterations 4.8273243E-02 1.776764 at 60iterations 2.0948896E-02 0.7369347 at 70iterations 9.0870662E-03 0.3690491 at 80iterations 3.9811283E-03 0.1581497 at 90iterations 1.7604275E-03 6.4105988E-02 at 100iterations 7.9017709E-04 2.6920915E-02 at 110iterations 3.6555089E-04 1.3463974E-02 at 120iterations finished qdiffx linear iterations at : 01:11:08 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 3.6555089E-04 1.3463974E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 01:11:09 7.948u 0.190s 0:08.42 96.5% 0+0k 0+45240io 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 Sun Feb 12 2012 at 01:11:09 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2555 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: 2.576722 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): -11.81200 37.17300 ymin,ymax (A): -28.34400 22.17900 zmin,zma (A): 31.73700 93.90900 x,y,z range (A): 48.98500 50.52300 62.17200 scale (grids/A): 2.576722 object centre (A): 12.68050 -3.082500 62.82300 number of atom coordinates read : 2555 total number of charged atoms : 2339 net assigned charge : -7.999981 assigned positive charge : 329.3683 centred at (gu) : 96.54456 81.88500 94.85174 assigned negative charge : -337.3690 centred at (gu) : 96.24786 82.08226 96.04452 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 138561 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24849 grid for indexing accessible points = 1.400000 m= 61108 mr = 93460 m= 18802 mr = 45707 m= 3501 mr = 13102 m= 318 mr = 2083 m= 10 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 678 time to turn everything in is 0.9600000 number of dielectric boundary points 67827 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 18705 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) : 1.717815 object centre at (A) : 12.68050 -3.082500 62.82300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3152846 -0.5982574 midg,1,midg; midg,igrid,midg -3.8193376E-03 -2.5709696E-02 1,midg,midg; igrid,midg,midg -5.8727417E-02 -3.6348484E-02 gauss-seidel spectral radius is 0.9991896 estimated iterations to convergence 277 setup time was (sec) 1.190000 now iterating at: 01:11:10 rms-change max change #iterations 8.111414 296.0425 at 10iterations 4.693491 138.9971 at 20iterations 2.696638 77.79526 at 30iterations 1.541146 37.44801 at 40iterations 0.8741813 21.92315 at 50iterations 0.4957027 11.41275 at 60iterations 0.2802050 7.183495 at 70iterations 0.1583024 4.101001 at 80iterations 8.8965736E-02 2.045416 at 90iterations 5.0109278E-02 1.289920 at 100iterations 2.8143425E-02 0.6134720 at 110iterations 1.5812408E-02 0.3511376 at 120iterations 8.9006647E-03 0.2006512 at 130iterations 5.0094523E-03 0.1092907 at 140iterations 2.8272045E-03 6.6457748E-02 at 150iterations 1.6108198E-03 3.6012650E-02 at 160iterations 9.2327659E-04 2.0870686E-02 at 170iterations 5.3851848E-04 1.3122559E-02 at 180iterations finished qdiffx linear iterations at : 01:11:21 total time elapsed so far: 12.50000 # loops : 180 mean,max change (kT/e) : 5.3851848E-04 1.3122559E-02 energy calculations done at 12.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.64000 DelPhi exited at 01:11:22 12.643u 0.218s 0:13.17 97.5% 0+0k 0+45232io 0pf+0w