Sat Oct 15 14:32:52 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 Sat Oct 15 2011 at 14:32:52 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2828 !!! WARNING: HIT 107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5745271 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): -30.96100 31.00300 ymin,ymax (A): -21.58400 24.46900 zmin,zma (A): -9.066999 38.15100 x,y,z range (A): 61.96400 46.05300 47.21800 scale (grids/A): 0.5745271 object centre (A): 2.0999908E-02 1.442500 14.54200 number of atom coordinates read : 2828 total number of charged atoms : 2688 net assigned charge : -0.9859709 assigned positive charge : 429.5222 centred at (gu) : 90.92459 89.77248 89.89726 assigned negative charge : -430.5092 centred at (gu) : 90.89349 89.58779 89.78224 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6167 nv = 96 ne = 84 npr = 56544 no. pairs analyzed = 56544 no. exposed pairs = 3722 no. arc points = 26131 no. surface atoms = 1257 nbur = 1571 mkacc time = 9.9999994E-02 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= 252 mr = 3124 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 26 time to turn everything in is 0.2000000 number of dielectric boundary points 3288 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2725 ## 338 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7901 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2936011E-09 1.8000005E-09 midg,1,midg; midg,igrid,midg -3.7175052E-09 2.8759373E-09 1,midg,midg; igrid,midg,midg -5.8040783E-10 4.7999599E-10 gauss-seidel spectral radius is 0.9843578 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 14:32:54 rms-change max change #iterations 8.9285493E-02 14.06789 at 10iterations 6.7669163E-03 1.024825 at 20iterations 5.1154650E-04 8.8253975E-02 at 30iterations 4.0127230E-05 5.8212280E-03 at 40iterations 3.0983372E-06 4.7826767E-04 at 50iterations finished qdiffx linear iterations at : 14:33:01 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 3.0983372E-06 4.7826767E-04 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 14:33:02 3.639u 0.244s 0:10.62 36.4% 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 15 2011 at 14:33:03 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2828 !!! WARNING: HIT 107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.723581 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): -30.96100 31.00300 ymin,ymax (A): -21.58400 24.46900 zmin,zma (A): -9.066999 38.15100 x,y,z range (A): 61.96400 46.05300 47.21800 scale (grids/A): 1.723581 object centre (A): 2.0999908E-02 1.442500 14.54200 number of atom coordinates read : 2828 total number of charged atoms : 2688 net assigned charge : -0.9859709 assigned positive charge : 429.5222 centred at (gu) : 92.77296 89.31701 89.69130 assigned negative charge : -430.5092 centred at (gu) : 92.68014 88.76324 89.34675 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 67423 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26131 grid for indexing accessible points = 1.400000 m= 21049 mr = 44927 m= 2421 mr = 14383 m= 75 mr = 1261 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1929 time to turn everything in is 0.3400000 number of dielectric boundary points 30390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 272 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 20828 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) : 0.5745271 object centre at (A) : 2.0999908E-02 1.442500 14.54200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6182422E-03 8.8500790E-03 midg,1,midg; midg,igrid,midg -2.3501135E-02 1.2418970E-02 1,midg,midg; igrid,midg,midg -7.0910342E-03 3.6233407E-03 gauss-seidel spectral radius is 0.9983635 estimated iterations to convergence 196 setup time was (sec) 0.5900000 now iterating at: 14:33:06 rms-change max change #iterations 3.694986 198.8421 at 10iterations 1.601389 77.03264 at 20iterations 0.6948929 25.48281 at 30iterations 0.3032545 11.10640 at 40iterations 0.1318164 4.260763 at 50iterations 5.7119586E-02 2.256430 at 60iterations 2.4994995E-02 0.9054356 at 70iterations 1.0825595E-02 0.3866091 at 80iterations 4.7342195E-03 0.1657562 at 90iterations 2.0585705E-03 7.0093155E-02 at 100iterations 8.9544442E-04 3.3871651E-02 at 110iterations 3.8966624E-04 1.3557434E-02 at 120iterations finished qdiffx linear iterations at : 14:33:21 total time elapsed so far: 8.510000 # loops : 120 mean,max change (kT/e) : 3.8966624E-04 1.3557434E-02 energy calculations done at 8.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.650000 DelPhi exited at 14:33:22 8.652u 0.262s 0:19.28 46.2% 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 15 2011 at 14:33:22 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2828 !!! WARNING: HIT 107 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.585372 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): -30.96100 31.00300 ymin,ymax (A): -21.58400 24.46900 zmin,zma (A): -9.066999 38.15100 x,y,z range (A): 61.96400 46.05300 47.21800 scale (grids/A): 2.585372 object centre (A): 2.0999908E-02 1.442500 14.54200 number of atom coordinates read : 2828 total number of charged atoms : 2688 net assigned charge : -0.9859709 assigned positive charge : 429.5222 centred at (gu) : 94.15949 88.97525 89.53669 assigned negative charge : -430.5092 centred at (gu) : 94.02016 88.14475 89.02003 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 156365 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26131 grid for indexing accessible points = 1.400000 m= 71775 mr = 109940 m= 21399 mr = 56336 m= 3857 mr = 16141 m= 354 mr = 2539 m= 11 mr = 223 m= 0 mr = 4 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 6497 time to turn everything in is 0.8500000 number of dielectric boundary points 68578 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 21491 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) : 1.723581 object centre at (A) : 2.0999908E-02 1.442500 14.54200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0123169E-02 9.7815230E-02 midg,1,midg; midg,igrid,midg -0.2627895 0.1820857 1,midg,midg; igrid,midg,midg 3.9812114E-02 9.7106285E-02 gauss-seidel spectral radius is 0.9991947 estimated iterations to convergence 278 setup time was (sec) 1.110000 now iterating at: 14:33:25 rms-change max change #iterations 9.315321 323.0476 at 10iterations 5.330192 121.3097 at 20iterations 3.022566 65.00502 at 30iterations 1.710218 40.29254 at 40iterations 0.9670929 19.68877 at 50iterations 0.5454327 12.42319 at 60iterations 0.3068271 7.266781 at 70iterations 0.1725288 3.520199 at 80iterations 9.6553847E-02 2.022192 at 90iterations 5.4290362E-02 1.202799 at 100iterations 3.0441683E-02 0.6142292 at 110iterations 1.7052196E-02 0.3271503 at 120iterations 9.5540239E-03 0.2039986 at 130iterations 5.3506512E-03 0.1115678 at 140iterations 2.9933569E-03 6.2341690E-02 at 150iterations 1.6802493E-03 3.2063484E-02 at 160iterations 9.4045827E-04 1.8821239E-02 at 170iterations 5.2735204E-04 9.8390579E-03 at 180iterations finished qdiffx linear iterations at : 14:33:47 total time elapsed so far: 14.77000 # loops : 180 mean,max change (kT/e) : 5.2735204E-04 9.8390579E-03 energy calculations done at 14.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.91000 DelPhi exited at 14:33:47 14.907u 0.337s 0:25.05 60.7% 0+0k 0+0io 0pf+0w