Mon Oct 10 16:03:38 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 16:03:38 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 = 5172 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.4728070 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): 7.533000 62.66700 ymin,ymax (A): -28.87200 46.42300 zmin,zma (A): -29.12700 33.62900 x,y,z range (A): 55.13400 75.29500 62.75600 scale (grids/A): 0.4728070 object centre (A): 35.10000 8.775500 2.251000 number of atom coordinates read : 5172 total number of charged atoms : 5011 net assigned charge : 4.000034 assigned positive charge : 779.5355 centred at (gu) : 89.61611 88.96669 89.21317 assigned negative charge : -775.5403 centred at (gu) : 89.60912 88.95691 89.22893 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7002 nv = 96 ne = 84 npr = 106435 no. pairs analyzed = 106435 no. exposed pairs = 6227 no. arc points = 41720 no. surface atoms = 2111 nbur = 3061 mkacc time = 0.1800000 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 = 1.792000 m= 196 mr = 3683 m= 0 mr = 1 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3948 ## 736 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 9667 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1125022E-11 1.2068545E-12 midg,1,midg; midg,igrid,midg 5.7508113E-12 1.0498700E-11 1,midg,midg; igrid,midg,midg 6.3785865E-12 1.1343356E-11 gauss-seidel spectral radius is 0.9771629 estimated iterations to convergence 55 setup time was (sec) 0.5100000 now iterating at: 16:03:39 rms-change max change #iterations 4.7303047E-02 7.919273 at 10iterations 3.2421385E-03 0.5606842 at 20iterations 9.9045667E-04 0.1410637 at 30iterations 4.0923202E-04 5.5786133E-02 at 40iterations 1.7231879E-04 2.4186134E-02 at 50iterations finished qdiffx linear iterations at : 16:03:42 total time elapsed so far: 3.510000 # loops : 50 mean,max change (kT/e) : 1.7231879E-04 2.4186134E-02 energy calculations done at 3.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 16:03:42 3.647u 0.199s 0:04.13 92.7% 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 16:03:42 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 = 5172 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.418421 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): 7.533000 62.66700 ymin,ymax (A): -28.87200 46.42300 zmin,zma (A): -29.12700 33.62900 x,y,z range (A): 55.13400 75.29500 62.75600 scale (grids/A): 1.418421 object centre (A): 35.10000 8.775500 2.251000 number of atom coordinates read : 5172 total number of charged atoms : 5011 net assigned charge : 4.000034 assigned positive charge : 779.5355 centred at (gu) : 88.84657 86.89848 87.63829 assigned negative charge : -775.5403 centred at (gu) : 88.82705 86.87029 87.68624 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 81664 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41720 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 21638 mr = 57337 m= 1435 mr = 14063 m= 21 mr = 505 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 801 time to turn everything in is 0.4200000 number of dielectric boundary points 32853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 731 ## 20 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 36516 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) : 0.4728070 object centre at (A) : 35.10000 8.775500 2.251000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9009403E-04 -4.9033430E-03 midg,1,midg; midg,igrid,midg 1.6025923E-02 1.2154898E-02 1,midg,midg; igrid,midg,midg 1.4339040E-03 1.6672042E-03 gauss-seidel spectral radius is 0.9977742 estimated iterations to convergence 169 setup time was (sec) 0.6400000 now iterating at: 16:03:43 rms-change max change #iterations 3.268299 130.9080 at 10iterations 1.240505 45.13152 at 20iterations 0.4718720 15.73970 at 30iterations 0.1799145 6.407585 at 40iterations 6.8347231E-02 2.708490 at 50iterations 2.6287630E-02 0.9212246 at 60iterations 1.0296822E-02 0.3834877 at 70iterations 4.3024151E-03 0.1534042 at 80iterations 2.0574338E-03 8.0808640E-02 at 90iterations 1.1928892E-03 3.5625458E-02 at 100iterations 8.0362911E-04 2.3715973E-02 at 110iterations 5.6965172E-04 1.5679359E-02 at 120iterations finished qdiffx linear iterations at : 16:03:50 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 5.6965172E-04 1.5679359E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 16:03:51 8.012u 0.217s 0:08.59 95.6% 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 16:03:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5172 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.127631 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): 7.533000 62.66700 ymin,ymax (A): -28.87200 46.42300 zmin,zma (A): -29.12700 33.62900 x,y,z range (A): 55.13400 75.29500 62.75600 scale (grids/A): 2.127631 object centre (A): 35.10000 8.775500 2.251000 number of atom coordinates read : 5172 total number of charged atoms : 5011 net assigned charge : 4.000034 assigned positive charge : 779.5355 centred at (gu) : 88.26945 85.34734 86.45716 assigned negative charge : -775.5403 centred at (gu) : 88.24039 85.30545 86.52924 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 191420 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41720 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 81004 mr = 141624 m= 17578 mr = 62630 m= 1795 mr = 12311 m= 43 mr = 940 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 2656 time to turn everything in is 0.9800000 number of dielectric boundary points 74327 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 39814 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) : 1.418421 object centre at (A) : 35.10000 8.775500 2.251000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9346077E-02 -0.1164013 midg,1,midg; midg,igrid,midg 0.4197136 0.5014066 1,midg,midg; igrid,midg,midg 5.0874945E-02 5.1028762E-02 gauss-seidel spectral radius is 0.9990602 estimated iterations to convergence 258 setup time was (sec) 1.220000 now iterating at: 16:03:52 rms-change max change #iterations 9.340872 349.2976 at 10iterations 5.171113 125.7435 at 20iterations 2.836955 65.60677 at 30iterations 1.552377 36.73135 at 40iterations 0.8454284 18.03852 at 50iterations 0.4580038 10.98556 at 60iterations 0.2476184 4.985836 at 70iterations 0.1335937 2.918918 at 80iterations 7.2002366E-02 1.454728 at 90iterations 3.8898416E-02 0.7633486 at 100iterations 2.0985257E-02 0.4835844 at 110iterations 1.1315444E-02 0.2440243 at 120iterations 6.1419136E-03 0.1345921 at 130iterations 3.3700678E-03 7.4619293E-02 at 140iterations 1.8949771E-03 3.9396763E-02 at 150iterations 1.1158457E-03 2.4406433E-02 at 160iterations 7.0253527E-04 1.3412476E-02 at 170iterations 4.7796516E-04 9.1247559E-03 at 180iterations finished qdiffx linear iterations at : 16:04:04 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 4.7796516E-04 9.1247559E-03 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.98000 DelPhi exited at 16:04:04 12.982u 0.215s 0:13.47 97.9% 0+0k 0+0io 0pf+0w