Sat Oct 15 11:07:27 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 11:07:27 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4069 !!! WARNING: HIR 974 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5702204 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): 17.23400 76.05200 ymin,ymax (A): 25.29400 77.16200 zmin,zma (A): 7.850000 70.28200 x,y,z range (A): 58.81800 51.86800 62.43200 scale (grids/A): 0.5702204 object centre (A): 46.64300 51.22800 39.06600 number of atom coordinates read : 4069 total number of charged atoms : 3924 net assigned charge : -1.485958 assigned positive charge : 606.9514 centred at (gu) : 90.53518 90.38011 90.06936 assigned negative charge : -608.4396 centred at (gu) : 90.48495 90.50131 90.15520 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8709 nv = 96 ne = 84 npr = 84802 no. pairs analyzed = 84802 no. exposed pairs = 4715 no. arc points = 31443 no. surface atoms = 1610 nbur = 2459 mkacc time = 0.2200000 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= 406 mr = 5110 m= 0 mr = 38 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.4300000 number of dielectric boundary points 3967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3288 ## 364 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 11327 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5934088E-09 -2.1367978E-09 midg,1,midg; midg,igrid,midg 2.1594069E-09 -3.1652634E-09 1,midg,midg; igrid,midg,midg -1.1582145E-09 9.8240793E-10 gauss-seidel spectral radius is 0.9842103 estimated iterations to convergence 65 setup time was (sec) 0.7200000 now iterating at: 11:07:28 rms-change max change #iterations 0.1060767 15.22586 at 10iterations 8.4457193E-03 1.184399 at 20iterations 9.8710833E-04 0.1297073 at 30iterations 2.5092886E-04 2.5493622E-02 at 40iterations 8.1903738E-05 7.4954033E-03 at 50iterations finished qdiffx linear iterations at : 11:07:32 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 8.1903738E-05 7.4954033E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 11:07:32 4.276u 0.427s 0:05.02 93.4% 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 11:07:32 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4069 !!! WARNING: HIR 974 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.710661 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): 17.23400 76.05200 ymin,ymax (A): 25.29400 77.16200 zmin,zma (A): 7.850000 70.28200 x,y,z range (A): 58.81800 51.86800 62.43200 scale (grids/A): 1.710661 object centre (A): 46.64300 51.22800 39.06600 number of atom coordinates read : 4069 total number of charged atoms : 3924 net assigned charge : -1.485958 assigned positive charge : 606.9514 centred at (gu) : 91.60410 91.13933 90.20697 assigned negative charge : -608.4396 centred at (gu) : 91.45448 91.50348 90.46523 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 97757 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31443 grid for indexing accessible points = 1.400000 m= 34383 mr = 71634 m= 4280 mr = 25478 m= 143 mr = 2525 m= 0 mr = 40 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1924 time to turn everything in is 0.7400000 number of dielectric boundary points 36886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 292 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 30390 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) : 0.5702204 object centre at (A) : 46.64300 51.22800 39.06600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2614336E-02 -2.2740172E-02 midg,1,midg; midg,igrid,midg 1.3458724E-02 -3.2787979E-02 1,midg,midg; igrid,midg,midg 1.7465046E-03 1.2474161E-02 gauss-seidel spectral radius is 0.9984555 estimated iterations to convergence 202 setup time was (sec) 1.040000 now iterating at: 11:07:34 rms-change max change #iterations 4.422922 156.1749 at 10iterations 1.966746 64.06850 at 20iterations 0.8808750 23.61654 at 30iterations 0.3937747 11.77083 at 40iterations 0.1766748 4.809228 at 50iterations 7.8830950E-02 2.471180 at 60iterations 3.5422582E-02 1.017901 at 70iterations 1.5899654E-02 0.4490681 at 80iterations 7.1714125E-03 0.2109983 at 90iterations 3.2805176E-03 9.9666119E-02 at 100iterations 1.5398753E-03 4.3939590E-02 at 110iterations 7.5243891E-04 2.2472382E-02 at 120iterations finished qdiffx linear iterations at : 11:07:43 total time elapsed so far: 9.890000 # loops : 120 mean,max change (kT/e) : 7.5243891E-04 2.2472382E-02 energy calculations done at 9.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.06000 DelPhi exited at 11:07:43 10.065u 0.487s 0:10.87 96.9% 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 11:07:43 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4069 !!! WARNING: HIR 974 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.565992 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): 17.23400 76.05200 ymin,ymax (A): 25.29400 77.16200 zmin,zma (A): 7.850000 70.28200 x,y,z range (A): 58.81800 51.86800 62.43200 scale (grids/A): 2.565992 object centre (A): 46.64300 51.22800 39.06600 number of atom coordinates read : 4069 total number of charged atoms : 3924 net assigned charge : -1.485958 assigned positive charge : 606.9514 centred at (gu) : 92.40611 91.70887 90.30997 assigned negative charge : -608.4396 centred at (gu) : 92.18152 92.25509 90.69787 start vw surface at 0.1500000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 226887 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31443 grid for indexing accessible points = 1.400000 m= 115798 mr = 173322 m= 37382 mr = 95983 m= 7347 mr = 29851 m= 681 mr = 5400 m= 22 mr = 384 m= 0 mr = 10 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 6423 time to turn everything in is 1.940000 number of dielectric boundary points 83167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 2.090000 number of grid points assigned charge 31371 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) : 1.710661 object centre at (A) : 46.64300 51.22800 39.06600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1764240 -0.5634433 midg,1,midg; midg,igrid,midg 0.1932582 -0.4140657 1,midg,midg; igrid,midg,midg 0.1633722 0.1605842 gauss-seidel spectral radius is 0.9992358 estimated iterations to convergence 286 setup time was (sec) 2.280000 now iterating at: 11:07:46 rms-change max change #iterations 10.96146 328.1514 at 10iterations 6.389022 118.8232 at 20iterations 3.691321 77.05064 at 30iterations 2.133658 42.31011 at 40iterations 1.226496 19.89387 at 50iterations 0.7046570 13.79138 at 60iterations 0.4040450 7.927678 at 70iterations 0.2309355 4.029487 at 80iterations 0.1319857 2.185322 at 90iterations 7.5481243E-02 1.259514 at 100iterations 4.3220028E-02 0.8741085 at 110iterations 2.4687877E-02 0.4289815 at 120iterations 1.4142858E-02 0.2791061 at 130iterations 8.1614992E-03 0.1303215 at 140iterations 4.7285650E-03 8.5096836E-02 at 150iterations 2.7813693E-03 5.5595398E-02 at 160iterations 1.6715187E-03 3.1173706E-02 at 170iterations 1.0440683E-03 1.8512726E-02 at 180iterations finished qdiffx linear iterations at : 11:08:01 total time elapsed so far: 17.60000 # loops : 180 mean,max change (kT/e) : 1.0440683E-03 1.8512726E-02 energy calculations done at 17.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.77000 DelPhi exited at 11:08:02 17.774u 0.522s 0:18.60 98.3% 0+0k 0+0io 0pf+0w