Mon Oct 10 18:51:07 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 Mon Oct 10 2011 at 18:51:07 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 = 2356 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: 0.6254721 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): 48.02500 101.4600 ymin,ymax (A): 12.28600 69.20300 zmin,zma (A): 20.52700 64.29500 x,y,z range (A): 53.43500 56.91700 43.76800 scale (grids/A): 0.6254721 object centre (A): 74.74250 40.74450 42.41100 number of atom coordinates read : 2356 total number of charged atoms : 2218 net assigned charge : 2.000005 assigned positive charge : 350.9539 centred at (gu) : 89.50596 88.19704 91.35017 assigned negative charge : -348.9546 centred at (gu) : 89.41862 88.20337 91.48935 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6259 nv = 96 ne = 84 npr = 47147 no. pairs analyzed = 47147 no. exposed pairs = 3011 no. arc points = 20536 no. surface atoms = 1019 nbur = 1337 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 365 mr = 3488 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.3000000 number of dielectric boundary points 3101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2009 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7514 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.6295016E-09 -1.0547803E-08 midg,1,midg; midg,igrid,midg 3.7074488E-09 1.1231545E-09 1,midg,midg; igrid,midg,midg -4.5460595E-09 7.2535160E-09 gauss-seidel spectral radius is 0.9867420 estimated iterations to convergence 71 setup time was (sec) 0.5600000 now iterating at: 18:51:08 rms-change max change #iterations 0.1217898 17.11477 at 10iterations 1.1791327E-02 1.716036 at 20iterations 1.2772701E-03 0.2014732 at 30iterations 2.1451387E-04 3.7565231E-02 at 40iterations 5.1861964E-05 9.5086098E-03 at 50iterations finished qdiffx linear iterations at : 18:51:11 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 5.1861964E-05 9.5086098E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 18:51:11 3.570u 0.167s 0:04.06 91.8% 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 Mon Oct 10 2011 at 18:51:11 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 = 2356 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: 1.876416 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): 48.02500 101.4600 ymin,ymax (A): 12.28600 69.20300 zmin,zma (A): 20.52700 64.29500 x,y,z range (A): 53.43500 56.91700 43.76800 scale (grids/A): 1.876416 object centre (A): 74.74250 40.74450 42.41100 number of atom coordinates read : 2356 total number of charged atoms : 2218 net assigned charge : 2.000005 assigned positive charge : 350.9539 centred at (gu) : 88.51756 84.59060 94.04976 assigned negative charge : -348.9546 centred at (gu) : 88.25568 84.60993 94.46789 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 67839 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20536 grid for indexing accessible points = 1.400000 m= 25770 mr = 47568 m= 4310 mr = 19168 m= 212 mr = 2730 m= 3 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 456 time to turn everything in is 0.5500000 number of dielectric boundary points 28626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17399 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) : 0.6254721 object centre at (A) : 74.74250 40.74450 42.41100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5255694E-02 -8.6225020E-03 midg,1,midg; midg,igrid,midg -1.6863065E-02 2.1729298E-02 1,midg,midg; igrid,midg,midg -1.3999992E-02 3.5057727E-02 gauss-seidel spectral radius is 0.9985717 estimated iterations to convergence 210 setup time was (sec) 0.8500000 now iterating at: 18:51:12 rms-change max change #iterations 3.873890 185.8195 at 10iterations 1.776018 68.92629 at 20iterations 0.8205138 28.43479 at 30iterations 0.3785379 15.30862 at 40iterations 0.1738134 5.753906 at 50iterations 7.9995818E-02 2.683243 at 60iterations 3.6978889E-02 1.295929 at 70iterations 1.7033903E-02 0.6212654 at 80iterations 7.9206461E-03 0.2558308 at 90iterations 3.6872386E-03 0.1205673 at 100iterations 1.7426061E-03 5.9146881E-02 at 110iterations 8.4402284E-04 2.7194977E-02 at 120iterations finished qdiffx linear iterations at : 18:51:19 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 8.4402284E-04 2.7194977E-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) 7.990000 DelPhi exited at 18:51:20 7.991u 0.213s 0:08.51 96.3% 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 Mon Oct 10 2011 at 18:51:20 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 = 2356 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: 2.814625 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): 48.02500 101.4600 ymin,ymax (A): 12.28600 69.20300 zmin,zma (A): 20.52700 64.29500 x,y,z range (A): 53.43500 56.91700 43.76800 scale (grids/A): 2.814625 object centre (A): 74.74250 40.74450 42.41100 number of atom coordinates read : 2356 total number of charged atoms : 2218 net assigned charge : 2.000005 assigned positive charge : 350.9539 centred at (gu) : 87.77608 81.88570 96.07460 assigned negative charge : -348.9546 centred at (gu) : 87.38355 81.91479 96.70177 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 156864 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20536 grid for indexing accessible points = 1.400000 m= 81531 mr = 115398 m= 31638 mr = 67017 m= 7915 mr = 25625 m= 1012 mr = 5937 m= 40 mr = 616 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.8100001 no. cavity mid-points inaccessible to solvent = 1663 time to turn everything in is 1.360000 number of dielectric boundary points 64405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 17742 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) : 1.876416 object centre at (A) : 74.74250 40.74450 42.41100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1632736 -5.1291350E-02 midg,1,midg; midg,igrid,midg -0.2910209 0.5078059 1,midg,midg; igrid,midg,midg -0.2374629 0.5963946 gauss-seidel spectral radius is 0.9992378 estimated iterations to convergence 286 setup time was (sec) 1.680000 now iterating at: 18:51:22 rms-change max change #iterations 9.284888 355.2594 at 10iterations 5.438513 137.4558 at 20iterations 3.153763 75.11137 at 30iterations 1.822424 41.82484 at 40iterations 1.047421 21.12991 at 50iterations 0.6012350 12.35921 at 60iterations 0.3451265 7.209491 at 70iterations 0.1975538 3.868675 at 80iterations 0.1129024 2.470908 at 90iterations 6.4736575E-02 1.234957 at 100iterations 3.6982883E-02 0.7614956 at 110iterations 2.1126300E-02 0.3899994 at 120iterations 1.2045976E-02 0.2475166 at 130iterations 6.8967221E-03 0.1344876 at 140iterations 3.9475299E-03 6.9642544E-02 at 150iterations 2.2717889E-03 4.8376083E-02 at 160iterations 1.3207668E-03 2.6780128E-02 at 170iterations 7.7856134E-04 1.5095592E-02 at 180iterations finished qdiffx linear iterations at : 18:51:33 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 7.7856134E-04 1.5095592E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 18:51:33 12.937u 0.222s 0:13.54 97.1% 0+0k 0+0io 0pf+0w