Sat Oct 8 11:33:02 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 Sat Oct 8 2011 at 11:33:02 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 = 4275 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: 0.5465907 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): -1.875000 61.07600 ymin,ymax (A): -15.14000 39.45800 zmin,zma (A): -19.97800 45.15300 x,y,z range (A): 62.95100 54.59800 65.13100 scale (grids/A): 0.5465907 object centre (A): 29.60050 12.15900 12.58750 number of atom coordinates read : 4275 total number of charged atoms : 4121 net assigned charge : -6.499957 assigned positive charge : 642.1447 centred at (gu) : 88.91491 90.42480 90.39585 assigned negative charge : -648.6475 centred at (gu) : 88.96850 90.52277 90.49506 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8130 nv = 96 ne = 84 npr = 89592 no. pairs analyzed = 89592 no. exposed pairs = 5005 no. arc points = 33160 no. surface atoms = 1709 nbur = 2566 mkacc time = 0.1500000 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 = 1.540000 m= 337 mr = 4626 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3381 ## 413 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 10802 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0570420E-10 -1.5513084E-09 midg,1,midg; midg,igrid,midg 4.9117732E-10 -1.5485675E-09 1,midg,midg; igrid,midg,midg 1.6094154E-10 -7.2448003E-10 gauss-seidel spectral radius is 0.9828300 estimated iterations to convergence 63 setup time was (sec) 0.5300000 now iterating at: 11:33:03 rms-change max change #iterations 8.8965699E-02 12.81158 at 10iterations 6.5581342E-03 0.9965916 at 20iterations 1.0242079E-03 0.1279833 at 30iterations 3.4437224E-04 4.6257019E-02 at 40iterations 1.2655499E-04 1.7524719E-02 at 50iterations finished qdiffx linear iterations at : 11:33:06 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 1.2655499E-04 1.7524719E-02 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.900000 DelPhi exited at 11:33:07 3.899u 0.238s 0:04.51 91.3% 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 Sat Oct 8 2011 at 11:33:07 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 = 4275 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: 1.639772 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): -1.875000 61.07600 ymin,ymax (A): -15.14000 39.45800 zmin,zma (A): -19.97800 45.15300 x,y,z range (A): 62.95100 54.59800 65.13100 scale (grids/A): 1.639772 object centre (A): 29.60050 12.15900 12.58750 number of atom coordinates read : 4275 total number of charged atoms : 4121 net assigned charge : -6.499957 assigned positive charge : 642.1447 centred at (gu) : 86.74377 91.27303 91.18625 assigned negative charge : -648.6475 centred at (gu) : 86.90524 91.56776 91.48488 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 91308 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33160 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 29641 mr = 65977 m= 3282 mr = 21154 m= 83 mr = 1728 m= 0 mr = 5 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 785 time to turn everything in is 0.4600000 number of dielectric boundary points 35450 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 322 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 31593 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) : 0.5465907 object centre at (A) : 29.60050 12.15900 12.58750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.9694108E-03 -2.1159597E-02 midg,1,midg; midg,igrid,midg -1.0200138E-02 -2.3703139E-02 1,midg,midg; igrid,midg,midg 1.6199689E-02 1.3147011E-02 gauss-seidel spectral radius is 0.9983222 estimated iterations to convergence 194 setup time was (sec) 0.7100000 now iterating at: 11:33:08 rms-change max change #iterations 4.139610 153.9155 at 10iterations 1.784557 57.56558 at 20iterations 0.7730804 24.43094 at 30iterations 0.3337748 9.624120 at 40iterations 0.1443996 4.731214 at 50iterations 6.2775016E-02 1.915756 at 60iterations 2.7215973E-02 0.8551886 at 70iterations 1.1864498E-02 0.3611336 at 80iterations 5.2325022E-03 0.1751940 at 90iterations 2.3924566E-03 7.1071625E-02 at 100iterations 1.1545834E-03 3.3871651E-02 at 110iterations 6.1230833E-04 2.0269275E-02 at 120iterations finished qdiffx linear iterations at : 11:33:16 total time elapsed so far: 8.860000 # loops : 120 mean,max change (kT/e) : 6.1230833E-04 2.0269275E-02 energy calculations done at 8.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.990000 DelPhi exited at 11:33:16 8.991u 0.266s 0:09.81 94.2% 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 11:33:17 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 = 4275 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: 2.459658 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): -1.875000 61.07600 ymin,ymax (A): -15.14000 39.45800 zmin,zma (A): -19.97800 45.15300 x,y,z range (A): 62.95100 54.59800 65.13100 scale (grids/A): 2.459658 object centre (A): 29.60050 12.15900 12.58750 number of atom coordinates read : 4275 total number of charged atoms : 4121 net assigned charge : -6.499957 assigned positive charge : 642.1447 centred at (gu) : 85.11516 91.90926 91.77905 assigned negative charge : -648.6475 centred at (gu) : 85.35769 92.35147 92.22724 start vw surface at 0.1100000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 212888 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33160 grid for indexing accessible points = 1.400000 m= 102765 mr = 161030 m= 30173 mr = 83518 m= 5299 mr = 23151 m= 359 mr = 3603 m= 4 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 2729 time to turn everything in is 1.120000 number of dielectric boundary points 80045 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 29 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 32930 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) : 1.639772 object centre at (A) : 29.60050 12.15900 12.58750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3827377 -0.2713636 midg,1,midg; midg,igrid,midg -0.2288768 -0.3193443 1,midg,midg; igrid,midg,midg 0.3719457 0.2624368 gauss-seidel spectral radius is 0.9992047 estimated iterations to convergence 280 setup time was (sec) 1.380000 now iterating at: 11:33:18 rms-change max change #iterations 10.76416 340.9453 at 10iterations 6.250666 127.7973 at 20iterations 3.598111 75.21593 at 30iterations 2.065659 44.75768 at 40iterations 1.178544 23.63380 at 50iterations 0.6698521 12.15525 at 60iterations 0.3815351 7.193298 at 70iterations 0.2163495 3.898853 at 80iterations 0.1224805 2.484999 at 90iterations 6.9295757E-02 1.269770 at 100iterations 3.9160945E-02 0.7053986 at 110iterations 2.2211608E-02 0.3805389 at 120iterations 1.2578757E-02 0.2330837 at 130iterations 7.1799052E-03 0.1263275 at 140iterations 4.1322098E-03 7.2752953E-02 at 150iterations 2.4196394E-03 4.5173645E-02 at 160iterations 1.4592991E-03 2.9157639E-02 at 170iterations 9.2048879E-04 1.8314362E-02 at 180iterations finished qdiffx linear iterations at : 11:33:31 total time elapsed so far: 13.92000 # loops : 180 mean,max change (kT/e) : 9.2048879E-04 1.8314362E-02 energy calculations done at 13.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.05000 DelPhi exited at 11:33:31 14.047u 0.274s 0:14.69 97.4% 0+0k 0+0io 0pf+0w