Tue Oct 11 06:54:51 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 Tue Oct 11 2011 at 06:54:51 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2968 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5436110 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): -19.72300 45.76500 ymin,ymax (A): 21.65400 76.57600 zmin,zma (A): -72.72600 -23.59700 x,y,z range (A): 65.48800 54.92200 49.12900 scale (grids/A): 0.5436110 object centre (A): 13.02100 49.11500 -48.16150 number of atom coordinates read : 2968 total number of charged atoms : 2826 net assigned charge : -1.960989 assigned positive charge : 434.5476 centred at (gu) : 89.14566 90.31818 90.02062 assigned negative charge : -436.5092 centred at (gu) : 89.09742 90.44818 90.02506 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5684 nv = 96 ne = 84 npr = 61322 no. pairs analyzed = 61322 no. exposed pairs = 3707 no. arc points = 25948 no. surface atoms = 1261 nbur = 1707 mkacc time = 0.1700000 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 = 1.596000 m= 235 mr = 2957 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 2950 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2621 ## 316 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7427 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.8198760E-11 -1.3222931E-10 midg,1,midg; midg,igrid,midg 6.0696226E-10 -9.6832364E-10 1,midg,midg; igrid,midg,midg -4.8905824E-10 1.4516296E-10 gauss-seidel spectral radius is 0.9825563 estimated iterations to convergence 62 setup time was (sec) 0.6600000 now iterating at: 06:54:52 rms-change max change #iterations 7.2383150E-02 12.03118 at 10iterations 4.8018266E-03 0.9226513 at 20iterations 3.5241744E-04 6.2568665E-02 at 30iterations 3.9226416E-05 8.5954666E-03 at 40iterations 7.1443283E-06 1.7538071E-03 at 50iterations finished qdiffx linear iterations at : 06:54:55 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 7.1443283E-06 1.7538071E-03 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 06:54:56 4.238u 0.269s 0:05.01 89.6% 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 Tue Oct 11 2011 at 06:54:56 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 # of charge parameter records: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2968 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.630833 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): -19.72300 45.76500 ymin,ymax (A): 21.65400 76.57600 zmin,zma (A): -72.72600 -23.59700 x,y,z range (A): 65.48800 54.92200 49.12900 scale (grids/A): 1.630833 object centre (A): 13.02100 49.11500 -48.16150 number of atom coordinates read : 2968 total number of charged atoms : 2826 net assigned charge : -1.960989 assigned positive charge : 434.5476 centred at (gu) : 87.43659 90.95397 90.06139 assigned negative charge : -436.5092 centred at (gu) : 87.29173 91.34428 90.07463 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 62700 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25948 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19755 mr = 42408 m= 2197 mr = 13919 m= 48 mr = 1180 m= 0 mr = 8 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 195 time to turn everything in is 0.5800000 number of dielectric boundary points 27185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 296 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 21675 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) : 0.5436110 object centre at (A) : 13.02100 49.11500 -48.16150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5866724E-03 9.6954154E-03 midg,1,midg; midg,igrid,midg -1.2591963E-03 1.3889440E-03 1,midg,midg; igrid,midg,midg -3.7156239E-03 -1.9264964E-02 gauss-seidel spectral radius is 0.9981822 estimated iterations to convergence 186 setup time was (sec) 0.9000000 now iterating at: 06:54:57 rms-change max change #iterations 3.262525 145.5373 at 10iterations 1.363520 56.64435 at 20iterations 0.5689805 21.09106 at 30iterations 0.2373986 9.640816 at 40iterations 9.8751925E-02 3.746796 at 50iterations 4.1322015E-02 1.481426 at 60iterations 1.7200217E-02 0.6459980 at 70iterations 7.1592801E-03 0.2499752 at 80iterations 2.9948528E-03 0.1380310 at 90iterations 1.2521486E-03 4.6222687E-02 at 100iterations 5.2326469E-04 1.9465446E-02 at 110iterations 2.1691753E-04 8.0299377E-03 at 120iterations finished qdiffx linear iterations at : 06:55:05 total time elapsed so far: 9.090000 # loops : 120 mean,max change (kT/e) : 2.1691753E-04 8.0299377E-03 energy calculations done at 9.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.270000 DelPhi exited at 06:55:06 9.271u 0.295s 0:09.87 96.8% 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 Tue Oct 11 2011 at 06:55:06 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2968 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.446250 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): -19.72300 45.76500 ymin,ymax (A): 21.65400 76.57600 zmin,zma (A): -72.72600 -23.59700 x,y,z range (A): 65.48800 54.92200 49.12900 scale (grids/A): 2.446250 object centre (A): 13.02100 49.11500 -48.16150 number of atom coordinates read : 2968 total number of charged atoms : 2826 net assigned charge : -1.960989 assigned positive charge : 434.5476 centred at (gu) : 86.15475 91.43063 90.09209 assigned negative charge : -436.5092 centred at (gu) : 85.93764 92.01648 90.11180 start vw surface at 0.1600000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 145563 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25948 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 67856 mr = 103795 m= 20271 mr = 54095 m= 3523 mr = 15659 m= 244 mr = 2471 m= 6 mr = 126 m= 0 mr = 4 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 761 time to turn everything in is 1.400000 number of dielectric boundary points 61313 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 22581 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) : 1.630833 object centre at (A) : 13.02100 49.11500 -48.16150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3089337E-02 0.1750778 midg,1,midg; midg,igrid,midg -2.3087036E-02 9.9895388E-02 1,midg,midg; igrid,midg,midg -7.8878097E-02 -0.5941704 gauss-seidel spectral radius is 0.9991367 estimated iterations to convergence 269 setup time was (sec) 1.720000 now iterating at: 06:55:08 rms-change max change #iterations 8.451316 260.1519 at 10iterations 4.712046 146.0892 at 20iterations 2.620170 73.88165 at 30iterations 1.450566 33.00930 at 40iterations 0.8030820 19.39817 at 50iterations 0.4418337 9.249256 at 60iterations 0.2441632 5.172955 at 70iterations 0.1339642 3.014992 at 80iterations 7.3718123E-02 1.604980 at 90iterations 4.0465727E-02 0.8260670 at 100iterations 2.2243083E-02 0.4898777 at 110iterations 1.2235367E-02 0.2625484 at 120iterations 6.7205052E-03 0.1470652 at 130iterations 3.6860679E-03 7.6087952E-02 at 140iterations 2.0196137E-03 4.2985916E-02 at 150iterations 1.1110955E-03 2.2550583E-02 at 160iterations 6.1053300E-04 1.2418747E-02 at 170iterations 3.3543500E-04 7.4329376E-03 at 180iterations finished qdiffx linear iterations at : 06:55:21 total time elapsed so far: 15.23000 # loops : 180 mean,max change (kT/e) : 3.3543500E-04 7.4329376E-03 energy calculations done at 15.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.40000 DelPhi exited at 06:55:22 15.404u 0.302s 0:16.02 98.0% 0+0k 0+0io 0pf+0w