Wed Dec 28 11:01:49 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+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 Wed Dec 28 2011 at 11:01:49 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6313512 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): -10.95600 35.27600 ymin,ymax (A): 1.601000 41.29000 zmin,zma (A): -19.33100 37.05600 x,y,z range (A): 46.23200 39.68900 56.38700 scale (grids/A): 0.6313512 object centre (A): 12.16000 21.44550 8.862500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.8260 centred at (gu) : 89.84265 89.49699 89.97181 assigned negative charge : -289.8262 centred at (gu) : 89.93403 89.63715 89.95453 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5389 nv = 96 ne = 84 npr = 40059 no. pairs analyzed = 40059 no. exposed pairs = 2399 no. arc points = 16715 no. surface atoms = 819 nbur = 1145 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 297 mr = 3089 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 2550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1682 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6295 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0268421E-09 3.3733714E-09 midg,1,midg; midg,igrid,midg 1.3045846E-08 -6.7560890E-09 1,midg,midg; igrid,midg,midg 8.7132275E-09 -3.9816186E-09 gauss-seidel spectral radius is 0.9869485 estimated iterations to convergence 72 setup time was (sec) 0.6500000 now iterating at: 11:01:50 rms-change max change #iterations 0.1215498 19.90304 at 10iterations 1.1385746E-02 2.217832 at 20iterations 1.1088882E-03 0.1723099 at 30iterations 1.0595344E-04 1.7108917E-02 at 40iterations 9.9363242E-06 1.5106201E-03 at 50iterations finished qdiffx linear iterations at : 11:01:56 total time elapsed so far: 6.300000 # loops : 50 mean,max change (kT/e) : 9.9363242E-06 1.5106201E-03 energy calculations done at 6.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.470000 DelPhi exited at 11:01:57 6.471u 0.586s 0:08.03 87.7% 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 Wed Dec 28 2011 at 11:01:57 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.894054 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): -10.95600 35.27600 ymin,ymax (A): 1.601000 41.29000 zmin,zma (A): -19.33100 37.05600 x,y,z range (A): 46.23200 39.68900 56.38700 scale (grids/A): 1.894054 object centre (A): 12.16000 21.44550 8.862500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.8260 centred at (gu) : 89.52792 88.49099 89.91528 assigned negative charge : -289.8262 centred at (gu) : 89.80235 88.91155 89.86387 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 57868 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16715 grid for indexing accessible points = 1.400000 m= 22193 mr = 40457 m= 3701 mr = 17335 m= 204 mr = 2542 m= 1 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 866 time to turn everything in is 0.5000000 number of dielectric boundary points 23555 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 14407 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) : 0.6313512 object centre at (A) : 12.16000 21.44550 8.862500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3628233E-02 3.4758504E-02 midg,1,midg; midg,igrid,midg 9.6400874E-04 -1.0957344E-02 1,midg,midg; igrid,midg,midg -2.3388022E-03 -5.1246574E-03 gauss-seidel spectral radius is 0.9985445 estimated iterations to convergence 208 setup time was (sec) 0.9800000 now iterating at: 11:01:59 rms-change max change #iterations 3.596685 169.7665 at 10iterations 1.644178 68.53536 at 20iterations 0.7530866 26.16243 at 30iterations 0.3440984 13.10429 at 40iterations 0.1569094 5.513157 at 50iterations 7.1720324E-02 2.524438 at 60iterations 3.2715745E-02 1.202892 at 70iterations 1.4992836E-02 0.4951153 at 80iterations 6.8318914E-03 0.2403841 at 90iterations 3.1313831E-03 0.1201630 at 100iterations 1.4249706E-03 4.7307968E-02 at 110iterations 6.5381627E-04 2.3036718E-02 at 120iterations finished qdiffx linear iterations at : 11:02:10 total time elapsed so far: 11.70000 # loops : 120 mean,max change (kT/e) : 6.5381627E-04 2.3036718E-02 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.87000 DelPhi exited at 11:02:11 11.875u 0.645s 0:13.55 92.3% 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 Wed Dec 28 2011 at 11:02:11 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.841080 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): -10.95600 35.27600 ymin,ymax (A): 1.601000 41.29000 zmin,zma (A): -19.33100 37.05600 x,y,z range (A): 46.23200 39.68900 56.38700 scale (grids/A): 2.841080 object centre (A): 12.16000 21.44550 8.862500 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 291.8260 centred at (gu) : 89.29186 87.73659 89.87288 assigned negative charge : -289.8262 centred at (gu) : 89.70343 88.36730 89.79582 start vw surface at 0.1100000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 133690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16715 grid for indexing accessible points = 1.400000 m= 70603 mr = 97770 m= 27577 mr = 59435 m= 6831 mr = 23302 m= 918 mr = 5453 m= 51 mr = 622 m= 0 mr = 24 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 2914 time to turn everything in is 1.300000 number of dielectric boundary points 53064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 14655 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) : 1.894054 object centre at (A) : 12.16000 21.44550 8.862500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2995870 0.2780404 midg,1,midg; midg,igrid,midg -3.7454650E-02 -0.1196715 1,midg,midg; igrid,midg,midg -5.8786497E-02 -7.5315528E-02 gauss-seidel spectral radius is 0.9992151 estimated iterations to convergence 282 setup time was (sec) 1.800000 now iterating at: 11:02:13 rms-change max change #iterations 8.525014 339.3827 at 10iterations 4.878400 119.1606 at 20iterations 2.773769 84.26950 at 30iterations 1.572551 38.94172 at 40iterations 0.8882664 19.31472 at 50iterations 0.5031753 10.21814 at 60iterations 0.2844771 5.588944 at 70iterations 0.1603262 3.464851 at 80iterations 9.0651743E-02 1.772977 at 90iterations 5.1202033E-02 1.042679 at 100iterations 2.8882788E-02 0.6471305 at 110iterations 1.6298711E-02 0.3557615 at 120iterations 9.1982270E-03 0.1987102 at 130iterations 5.1879385E-03 0.1111097 at 140iterations 2.9266884E-03 5.8552742E-02 at 150iterations 1.6517580E-03 3.6803722E-02 at 160iterations 9.3326037E-04 2.0919800E-02 at 170iterations 5.2576815E-04 1.0927200E-02 at 180iterations finished qdiffx linear iterations at : 11:02:34 total time elapsed so far: 22.24000 # loops : 180 mean,max change (kT/e) : 5.2576815E-04 1.0927200E-02 energy calculations done at 22.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.43000 DelPhi exited at 11:02:34 22.432u 0.599s 0:23.67 97.2% 0+0k 0+0io 0pf+0w