Mon Oct 10 14:10:00 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 Mon Oct 10 2011 at 14:10:00 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 # of charge parameter records: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2384 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6562575 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): 17.47300 71.72000 ymin,ymax (A): 26.45000 72.43501 zmin,zma (A): -112.1310 -62.23200 x,y,z range (A): 54.24700 45.98500 49.89900 scale (grids/A): 0.6562575 object centre (A): 44.59650 49.44250 -87.18150 number of atom coordinates read : 2384 total number of charged atoms : 2251 net assigned charge : -2.499994 assigned positive charge : 362.0352 centred at (gu) : 90.29533 89.26035 90.13840 assigned negative charge : -364.5358 centred at (gu) : 90.09155 89.29904 90.22997 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6869 nv = 96 ne = 84 npr = 49507 no. pairs analyzed = 49507 no. exposed pairs = 2911 no. arc points = 20635 no. surface atoms = 994 nbur = 1390 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 381 mr = 3816 m= 2 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 87 time to turn everything in is 0.1900000 number of dielectric boundary points 3383 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1966 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8170 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1837107E-09 -2.2075715E-08 midg,1,midg; midg,igrid,midg 8.4161778E-10 -1.0633444E-08 1,midg,midg; igrid,midg,midg -3.8503451E-08 2.9651909E-08 gauss-seidel spectral radius is 0.9879482 estimated iterations to convergence 74 setup time was (sec) 0.3700000 now iterating at: 14:10:00 rms-change max change #iterations 0.1601411 29.50670 at 10iterations 1.6956232E-02 2.839476 at 20iterations 1.7828126E-03 0.2728024 at 30iterations 2.0966151E-04 3.1021118E-02 at 40iterations 2.9762343E-05 4.6424866E-03 at 50iterations finished qdiffx linear iterations at : 14:10:03 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 2.9762343E-05 4.6424866E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 14:10:04 3.352u 0.162s 0:03.83 91.6% 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 Mon Oct 10 2011 at 14:10:04 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2384 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.968772 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): 17.47300 71.72000 ymin,ymax (A): 26.45000 72.43501 zmin,zma (A): -112.1310 -62.23200 x,y,z range (A): 54.24700 45.98500 49.89900 scale (grids/A): 1.968772 object centre (A): 44.59650 49.44250 -87.18150 number of atom coordinates read : 2384 total number of charged atoms : 2251 net assigned charge : -2.499994 assigned positive charge : 362.0352 centred at (gu) : 90.88565 87.78063 90.41496 assigned negative charge : -364.5358 centred at (gu) : 90.27470 87.89693 90.68990 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20635 grid for indexing accessible points = 1.400000 m= 27103 mr = 51781 m= 4855 mr = 20242 m= 389 mr = 3138 m= 13 mr = 192 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 3053 time to turn everything in is 0.3700000 number of dielectric boundary points 31289 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 84 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 17806 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) : 0.6562575 object centre at (A) : 44.59650 49.44250 -87.18150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1364152E-02 -3.1264275E-02 midg,1,midg; midg,igrid,midg 6.4140791E-03 -1.2278893E-02 1,midg,midg; igrid,midg,midg -7.5836219E-03 3.8111173E-02 gauss-seidel spectral radius is 0.9987000 estimated iterations to convergence 220 setup time was (sec) 0.5800000 now iterating at: 14:10:05 rms-change max change #iterations 4.418216 196.8431 at 10iterations 2.101881 74.80138 at 20iterations 0.9968779 30.96757 at 30iterations 0.4760357 15.38750 at 40iterations 0.2265659 7.029716 at 50iterations 0.1085669 3.391472 at 60iterations 5.1541656E-02 1.525316 at 70iterations 2.4638064E-02 0.7861400 at 80iterations 1.1726707E-02 0.3886061 at 90iterations 5.6201816E-03 0.1879209 at 100iterations 2.6922305E-03 9.5157623E-02 at 110iterations 1.2927916E-03 4.2064667E-02 at 120iterations finished qdiffx linear iterations at : 14:10:12 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 1.2927916E-03 4.2064667E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 14:10:12 7.763u 0.177s 0:08.24 96.2% 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 Mon Oct 10 2011 at 14:10:12 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2384 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.953159 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): 17.47300 71.72000 ymin,ymax (A): 26.45000 72.43501 zmin,zma (A): -112.1310 -62.23200 x,y,z range (A): 54.24700 45.98500 49.89900 scale (grids/A): 2.953159 object centre (A): 44.59650 49.44250 -87.18150 number of atom coordinates read : 2384 total number of charged atoms : 2251 net assigned charge : -2.499994 assigned positive charge : 362.0352 centred at (gu) : 91.32839 86.67074 90.62241 assigned negative charge : -364.5358 centred at (gu) : 90.41208 86.84547 91.03471 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 171761 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20635 grid for indexing accessible points = 1.400000 m= 87093 mr = 125335 m= 33001 mr = 71765 m= 9023 mr = 26861 m= 1726 mr = 6959 m= 144 mr = 1236 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 10565 time to turn everything in is 0.9500000 number of dielectric boundary points 70529 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 18008 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) : 1.968772 object centre at (A) : 44.59650 49.44250 -87.18150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3260558 -0.1740597 midg,1,midg; midg,igrid,midg 0.1575648 -5.7875272E-02 1,midg,midg; igrid,midg,midg 3.1161376E-03 0.5472489 gauss-seidel spectral radius is 0.9992667 estimated iterations to convergence 291 setup time was (sec) 1.200000 now iterating at: 14:10:13 rms-change max change #iterations 10.09480 357.0730 at 10iterations 5.900756 123.8683 at 20iterations 3.435431 73.25099 at 30iterations 2.000334 41.88165 at 40iterations 1.160552 22.59933 at 50iterations 0.6722918 12.49669 at 60iterations 0.3892747 7.439015 at 70iterations 0.2253943 4.037279 at 80iterations 0.1301803 2.512026 at 90iterations 7.4985646E-02 1.334596 at 100iterations 4.3371800E-02 0.8118963 at 110iterations 2.5019854E-02 0.4695396 at 120iterations 1.4418160E-02 0.2705612 at 130iterations 8.3293514E-03 0.1443386 at 140iterations 4.8075295E-03 8.1377506E-02 at 150iterations 2.7791501E-03 5.1563263E-02 at 160iterations 1.6093648E-03 2.8159142E-02 at 170iterations 9.3336269E-04 1.7157078E-02 at 180iterations finished qdiffx linear iterations at : 14:10:25 total time elapsed so far: 12.38000 # loops : 180 mean,max change (kT/e) : 9.3336269E-04 1.7157078E-02 energy calculations done at 12.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.50000 DelPhi exited at 14:10:25 12.505u 0.184s 0:13.18 96.2% 0+0k 0+0io 0pf+0w