Tue Oct 11 01:08:59 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 Tue Oct 11 2011 at 01:08:59 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 = 2746 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-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): -6.403000 37.40400 ymin,ymax (A): -20.68600 41.27800 zmin,zma (A): 24.62800 77.36400 x,y,z range (A): 43.80700 61.96400 52.73600 scale (grids/A): 0.5745271 object centre (A): 15.50050 10.29600 50.99600 number of atom coordinates read : 2746 total number of charged atoms : 2602 net assigned charge : 5.500017 assigned positive charge : 413.9494 centred at (gu) : 90.16270 89.03999 89.42664 assigned negative charge : -408.4502 centred at (gu) : 90.36913 89.22687 89.41003 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5888 nv = 96 ne = 84 npr = 55820 no. pairs analyzed = 55820 no. exposed pairs = 3220 no. arc points = 22888 no. surface atoms = 1093 nbur = 1653 mkacc time = 0.1500000 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= 233 mr = 3261 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.3200000 number of dielectric boundary points 2839 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2334 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7574 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.8711304E-10 1.0964784E-09 midg,1,midg; midg,igrid,midg 5.0922200E-09 -1.7755274E-09 1,midg,midg; igrid,midg,midg 4.1976662E-09 -2.6966811E-09 gauss-seidel spectral radius is 0.9843422 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 01:09:00 rms-change max change #iterations 9.0912305E-02 14.75967 at 10iterations 7.7263559E-03 1.414616 at 20iterations 9.8051457E-04 0.2447968 at 30iterations 2.1534956E-04 5.7102203E-02 at 40iterations 5.0477858E-05 1.3916016E-02 at 50iterations finished qdiffx linear iterations at : 01:09:04 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 5.0477858E-05 1.3916016E-02 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 01:09:04 4.453u 0.409s 0:05.15 94.1% 0+0k 0+0io 6pf+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 01:09:05 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 = 2746 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-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): -6.403000 37.40400 ymin,ymax (A): -20.68600 41.27800 zmin,zma (A): 24.62800 77.36400 x,y,z range (A): 43.80700 61.96400 52.73600 scale (grids/A): 1.723581 object centre (A): 15.50050 10.29600 50.99600 number of atom coordinates read : 2746 total number of charged atoms : 2602 net assigned charge : 5.500017 assigned positive charge : 413.9494 centred at (gu) : 90.48734 87.11916 88.27920 assigned negative charge : -408.4502 centred at (gu) : 91.10723 87.68007 88.22997 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 64978 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22888 grid for indexing accessible points = 1.400000 m= 20583 mr = 45216 m= 2398 mr = 14908 m= 69 mr = 1381 m= 0 mr = 11 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 4422 time to turn everything in is 0.5300000 number of dielectric boundary points 26512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 242 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 20159 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) : 15.50050 10.29600 50.99600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0650753E-03 9.2933308E-03 midg,1,midg; midg,igrid,midg -1.4697572E-02 -9.1660973E-03 1,midg,midg; igrid,midg,midg 2.0255176E-02 -8.3767890E-04 gauss-seidel spectral radius is 0.9983473 estimated iterations to convergence 195 setup time was (sec) 0.8900000 now iterating at: 01:09:06 rms-change max change #iterations 3.553494 153.0044 at 10iterations 1.539305 65.39763 at 20iterations 0.6704401 24.61640 at 30iterations 0.2902009 12.02770 at 40iterations 0.1263104 5.026402 at 50iterations 5.4865241E-02 2.209601 at 60iterations 2.4031529E-02 0.8637943 at 70iterations 1.0591761E-02 0.4140472 at 80iterations 4.7229575E-03 0.1602020 at 90iterations 2.1665036E-03 7.9277039E-02 at 100iterations 1.0480626E-03 4.7332764E-02 at 110iterations 5.4447475E-04 2.6618958E-02 at 120iterations finished qdiffx linear iterations at : 01:09:15 total time elapsed so far: 10.22000 # loops : 120 mean,max change (kT/e) : 5.4447475E-04 2.6618958E-02 energy calculations done at 10.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.39000 DelPhi exited at 01:09:16 10.399u 0.420s 0:11.48 94.1% 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 01:09:16 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 = 2746 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-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): -6.403000 37.40400 ymin,ymax (A): -20.68600 41.27800 zmin,zma (A): 24.62800 77.36400 x,y,z range (A): 43.80700 61.96400 52.73600 scale (grids/A): 2.585372 object centre (A): 15.50050 10.29600 50.99600 number of atom coordinates read : 2746 total number of charged atoms : 2602 net assigned charge : 5.500017 assigned positive charge : 413.9494 centred at (gu) : 90.73078 85.67873 87.41866 assigned negative charge : -408.4502 centred at (gu) : 91.66069 86.51993 87.34496 start vw surface at 0.1200000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 150816 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22888 grid for indexing accessible points = 1.400000 m= 70670 mr = 110009 m= 21367 mr = 57553 m= 3968 mr = 16767 m= 343 mr = 2902 m= 6 mr = 182 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 14822 time to turn everything in is 1.310000 number of dielectric boundary points 59757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 20807 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) : 15.50050 10.29600 50.99600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5136392E-02 8.5730106E-02 midg,1,midg; midg,igrid,midg -0.5761548 -0.1265468 1,midg,midg; igrid,midg,midg 0.2344927 2.3068944E-02 gauss-seidel spectral radius is 0.9991738 estimated iterations to convergence 275 setup time was (sec) 1.640000 now iterating at: 01:09:18 rms-change max change #iterations 8.810779 258.6572 at 10iterations 4.921047 118.2715 at 20iterations 2.759560 61.70644 at 30iterations 1.542654 34.72377 at 40iterations 0.8578290 17.47183 at 50iterations 0.4800699 10.31107 at 60iterations 0.2660207 5.465134 at 70iterations 0.1484387 3.130737 at 80iterations 8.2703955E-02 1.825618 at 90iterations 4.5993406E-02 0.9337635 at 100iterations 2.5697345E-02 0.5044155 at 110iterations 1.4350259E-02 0.3062735 at 120iterations 8.0616493E-03 0.1640205 at 130iterations 4.5692679E-03 0.1013947 at 140iterations 2.6220591E-03 7.0343018E-02 at 150iterations 1.5519940E-03 4.1851044E-02 at 160iterations 9.5372071E-04 2.5703430E-02 at 170iterations 6.1362068E-04 1.6921997E-02 at 180iterations finished qdiffx linear iterations at : 01:09:34 total time elapsed so far: 17.37000 # loops : 180 mean,max change (kT/e) : 6.1362068E-04 1.6921997E-02 energy calculations done at 17.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.54000 DelPhi exited at 01:09:35 17.540u 0.463s 0:18.57 96.9% 0+0k 0+0io 0pf+0w