Tue Nov 22 14:10:54 PST 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 Tue Nov 22 2011 at 14:10:58 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1952 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: 0.5922475 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): -19.91700 40.19300 ymin,ymax (A): -17.71100 25.38200 zmin,zma (A): -18.14600 23.84500 x,y,z range (A): 60.11000 43.09300 41.99100 scale (grids/A): 0.5922475 object centre (A): 10.13800 3.835500 2.849500 number of atom coordinates read : 1952 total number of charged atoms : 1818 net assigned charge : -1.999997 assigned positive charge : 288.0980 centred at (gu) : 91.48060 89.22488 89.69688 assigned negative charge : -290.0982 centred at (gu) : 91.47264 89.20978 89.79452 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4546 nv = 96 ne = 84 npr = 39670 no. pairs analyzed = 39670 no. exposed pairs = 2506 no. arc points = 17489 no. surface atoms = 854 nbur = 1098 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 = 1.484000 m= 206 mr = 2407 m= 0 mr = 21 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2200000 number of dielectric boundary points 2324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1767 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 5621 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4958448E-09 -2.5861819E-09 midg,1,midg; midg,igrid,midg -1.1810032E-09 -2.9386030E-10 1,midg,midg; igrid,midg,midg -6.0218736E-10 -6.9001649E-10 gauss-seidel spectral radius is 0.9851943 estimated iterations to convergence 67 setup time was (sec) 0.4600000 now iterating at: 14:11:02 rms-change max change #iterations 8.5792728E-02 16.09721 at 10iterations 7.0821969E-03 1.176231 at 20iterations 5.7699153E-04 9.3833923E-02 at 30iterations 4.6373629E-05 7.4546337E-03 at 40iterations 3.8746857E-06 7.4768066E-04 at 50iterations finished qdiffx linear iterations at : 14:11:10 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 3.8746857E-06 7.4768066E-04 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 14:11:13 3.235u 0.151s 0:15.50 21.8% 0+0k 0+0io 3pf+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 Nov 22 2011 at 14:11:15 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1952 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: 1.776743 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): -19.91700 40.19300 ymin,ymax (A): -17.71100 25.38200 zmin,zma (A): -18.14600 23.84500 x,y,z range (A): 60.11000 43.09300 41.99100 scale (grids/A): 1.776743 object centre (A): 10.13800 3.835500 2.849500 number of atom coordinates read : 1952 total number of charged atoms : 1818 net assigned charge : -1.999997 assigned positive charge : 288.0980 centred at (gu) : 94.44180 87.67474 89.09068 assigned negative charge : -290.0982 centred at (gu) : 94.41830 87.62943 89.38382 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 49389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17489 grid for indexing accessible points = 1.400000 m= 16682 mr = 33357 m= 2219 mr = 12308 m= 92 mr = 1361 m= 0 mr = 20 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 552 time to turn everything in is 0.3500000 number of dielectric boundary points 21336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 187 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 14164 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) : 0.5922475 object centre at (A) : 10.13800 3.835500 2.849500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9004550E-03 -4.9772095E-03 midg,1,midg; midg,igrid,midg -7.6342793E-03 -7.9779299E-03 1,midg,midg; igrid,midg,midg 1.5476842E-03 6.8576150E-03 gauss-seidel spectral radius is 0.9983534 estimated iterations to convergence 196 setup time was (sec) 0.6300000 now iterating at: 14:11:20 rms-change max change #iterations 3.090910 175.4106 at 10iterations 1.339011 60.34876 at 20iterations 0.5820435 22.83983 at 30iterations 0.2521258 11.19677 at 40iterations 0.1094605 4.417722 at 50iterations 4.7366776E-02 2.103712 at 60iterations 2.0637250E-02 0.8338318 at 70iterations 9.0030599E-03 0.3565598 at 80iterations 3.9071231E-03 0.1442523 at 90iterations 1.6982745E-03 6.5232277E-02 at 100iterations 7.3718303E-04 2.9541016E-02 at 110iterations 3.1876873E-04 1.2869596E-02 at 120iterations finished qdiffx linear iterations at : 14:11:39 total time elapsed so far: 7.080000 # loops : 120 mean,max change (kT/e) : 3.1876873E-04 1.2869596E-02 energy calculations done at 7.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.240000 DelPhi exited at 14:11:43 7.242u 0.183s 0:28.11 26.3% 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 Tue Nov 22 2011 at 14:11:48 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1952 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: 2.665114 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): -19.91700 40.19300 ymin,ymax (A): -17.71100 25.38200 zmin,zma (A): -18.14600 23.84500 x,y,z range (A): 60.11000 43.09300 41.99100 scale (grids/A): 2.665114 object centre (A): 10.13800 3.835500 2.849500 number of atom coordinates read : 1952 total number of charged atoms : 1818 net assigned charge : -1.999997 assigned positive charge : 288.0980 centred at (gu) : 96.66268 86.51220 88.63607 assigned negative charge : -290.0982 centred at (gu) : 96.62744 86.44426 89.07584 start vw surface at 0.1000000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 114221 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17489 grid for indexing accessible points = 1.400000 m= 55119 mr = 81051 m= 18553 mr = 44862 m= 3795 mr = 15000 m= 412 mr = 2766 m= 18 mr = 296 m= 0 mr = 10 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 1671 time to turn everything in is 0.8400000 number of dielectric boundary points 48133 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 14543 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) : 1.776743 object centre at (A) : 10.13800 3.835500 2.849500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4872878E-02 -6.2075529E-02 midg,1,midg; midg,igrid,midg -7.5959086E-02 -9.5871598E-02 1,midg,midg; igrid,midg,midg 4.3400049E-02 0.2702074 gauss-seidel spectral radius is 0.9991589 estimated iterations to convergence 272 setup time was (sec) 1.120000 now iterating at: 14:11:54 rms-change max change #iterations 7.560192 259.8480 at 10iterations 4.235501 117.1478 at 20iterations 2.348277 54.83675 at 30iterations 1.299181 31.69452 at 40iterations 0.7200573 15.96879 at 50iterations 0.3979384 8.509865 at 60iterations 0.2203836 5.129752 at 70iterations 0.1217119 2.678623 at 80iterations 6.7411698E-02 1.604519 at 90iterations 3.7158776E-02 0.8385153 at 100iterations 2.0550363E-02 0.4405937 at 110iterations 1.1361362E-02 0.2426128 at 120iterations 6.2605310E-03 0.1304523 at 130iterations 3.4543141E-03 8.4895372E-02 at 140iterations 1.9114453E-03 4.2509973E-02 at 150iterations 1.0566419E-03 2.5425911E-02 at 160iterations 5.8365148E-04 1.2858391E-02 at 170iterations 3.2280947E-04 7.3833466E-03 at 180iterations finished qdiffx linear iterations at : 14:12:22 total time elapsed so far: 10.30000 # loops : 180 mean,max change (kT/e) : 3.2280947E-04 7.3833466E-03 energy calculations done at 10.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.48000 DelPhi exited at 14:12:28 10.478u 0.175s 0:40.95 25.9% 0+0k 0+0io 0pf+0w