Sat Oct 15 14:32:04 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 15 2011 at 14:32:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2828 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 : -0.9999727 assigned positive charge : 424.2802 centred at (gu) : 90.96084 89.81313 89.87468 assigned negative charge : -425.2813 centred at (gu) : 90.92760 89.62238 89.75539 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 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 = 8.9999996E-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 0.2100000 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 0.2900000 number of grid points assigned charge 7901 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3631266E-09 1.8335530E-09 midg,1,midg; midg,igrid,midg -3.7587227E-09 2.9606271E-09 1,midg,midg; igrid,midg,midg -6.0286487E-10 5.1812110E-10 gauss-seidel spectral radius is 0.9843578 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 14:32:04 rms-change max change #iterations 8.6653002E-02 13.65094 at 10iterations 6.5562911E-03 1.032494 at 20iterations 4.9606356E-04 8.4525108E-02 at 30iterations 3.9114679E-05 5.7086945E-03 at 40iterations 3.0066815E-06 4.6396255E-04 at 50iterations finished qdiffx linear iterations at : 14:32:09 total time elapsed so far: 3.670000 # loops : 50 mean,max change (kT/e) : 3.0066815E-06 4.6396255E-04 energy calculations done at 3.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.800000 DelPhi exited at 14:32:10 3.806u 0.208s 0:07.08 56.4% 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 14:32:11 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 = 2828 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 : -0.9999727 assigned positive charge : 424.2802 centred at (gu) : 92.88174 89.43897 89.62360 assigned negative charge : -425.2813 centred at (gu) : 92.78250 88.86698 89.26623 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 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 0.3500000 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 -3.7059970E-03 9.3991747E-03 midg,1,midg; midg,igrid,midg -2.4460938E-02 1.2694766E-02 1,midg,midg; igrid,midg,midg -7.2107320E-03 3.6518984E-03 gauss-seidel spectral radius is 0.9983635 estimated iterations to convergence 196 setup time was (sec) 0.5900000 now iterating at: 14:32:12 rms-change max change #iterations 3.625305 199.7502 at 10iterations 1.571481 77.05812 at 20iterations 0.6820203 25.30961 at 30iterations 0.2974758 10.84488 at 40iterations 0.1293306 4.264931 at 50iterations 5.6043584E-02 2.200443 at 60iterations 2.4515910E-02 0.9242744 at 70iterations 1.0624348E-02 0.3816471 at 80iterations 4.6445234E-03 0.1650848 at 90iterations 2.0200354E-03 6.9293976E-02 at 100iterations 8.7880710E-04 3.3293247E-02 at 110iterations 3.8228094E-04 1.2906075E-02 at 120iterations finished qdiffx linear iterations at : 14:32:24 total time elapsed so far: 8.320000 # loops : 120 mean,max change (kT/e) : 3.8228094E-04 1.2906075E-02 energy calculations done at 8.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.450000 DelPhi exited at 14:32:25 8.453u 0.254s 0:13.96 62.3% 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 15 2011 at 14:32:25 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 = 2828 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: 2.585372 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 : -0.9999727 assigned positive charge : 424.2802 centred at (gu) : 94.32270 89.15822 89.43516 assigned negative charge : -425.2813 centred at (gu) : 94.17372 88.30039 88.89924 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 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 = 0.4900000 no. cavity mid-points inaccessible to solvent = 6497 time to turn everything in is 0.8700000 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 0.9800000 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 -3.1346772E-02 0.1053053 midg,1,midg; midg,igrid,midg -0.2768209 0.1855976 1,midg,midg; igrid,midg,midg 3.8357269E-02 9.7039171E-02 gauss-seidel spectral radius is 0.9991947 estimated iterations to convergence 278 setup time was (sec) 1.150000 now iterating at: 14:32:26 rms-change max change #iterations 9.178084 323.0474 at 10iterations 5.252419 121.3098 at 20iterations 2.980874 63.99600 at 30iterations 1.687016 39.82962 at 40iterations 0.9541811 19.46793 at 50iterations 0.5382885 12.21106 at 60iterations 0.3028634 7.239368 at 70iterations 0.1703387 3.359548 at 80iterations 9.5339596E-02 2.024775 at 90iterations 5.3628072E-02 1.195343 at 100iterations 3.0062240E-02 0.6258774 at 110iterations 1.6842997E-02 0.3213177 at 120iterations 9.4383899E-03 0.1944630 at 130iterations 5.2849418E-03 0.1135427 at 140iterations 2.9574099E-03 6.1524391E-02 at 150iterations 1.6605058E-03 3.2091141E-02 at 160iterations 9.2938956E-04 1.8927574E-02 at 170iterations 5.2109867E-04 9.6912384E-03 at 180iterations finished qdiffx linear iterations at : 14:32:50 total time elapsed so far: 13.87000 # loops : 180 mean,max change (kT/e) : 5.2109867E-04 9.6912384E-03 energy calculations done at 13.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.00000 DelPhi exited at 14:32:51 14.005u 0.332s 0:26.21 54.6% 0+0k 0+0io 0pf+0w