Tue Oct 11 07:54:23 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 Tue Oct 11 2011 at 07:54:23 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: THS 97 has a net charge of 0.4660 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.6433076 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): -1.551000 53.78800 ymin,ymax (A): -22.78400 22.90800 zmin,zma (A): 8.827000 53.88100 x,y,z range (A): 55.33900 45.69200 45.05400 scale (grids/A): 0.6433076 object centre (A): 26.11850 6.1999321E-02 31.35400 number of atom coordinates read : 2380 total number of charged atoms : 2232 net assigned charge : 6.425008 assigned positive charge : 360.7343 centred at (gu) : 88.68876 90.37865 90.10357 assigned negative charge : -354.3098 centred at (gu) : 88.68382 90.28932 89.88499 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6636 nv = 96 ne = 84 npr = 48090 no. pairs analyzed = 48090 no. exposed pairs = 2839 no. arc points = 19949 no. surface atoms = 965 nbur = 1415 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3732 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1963 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7823 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5437518E-08 3.5848167E-08 midg,1,midg; midg,igrid,midg -1.9418081E-10 2.2238485E-08 1,midg,midg; igrid,midg,midg 1.2659910E-08 8.2668423E-09 gauss-seidel spectral radius is 0.9874592 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 07:54:23 rms-change max change #iterations 0.1469107 20.34915 at 10iterations 1.5089662E-02 2.354733 at 20iterations 1.6468505E-03 0.2558231 at 30iterations 1.9590638E-04 2.9190063E-02 at 40iterations 2.7908829E-05 4.2495728E-03 at 50iterations finished qdiffx linear iterations at : 07:54:26 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.7908829E-05 4.2495728E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 07:54:27 3.377u 0.174s 0:04.03 87.8% 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 07:54:27 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: THS 97 has a net charge of 0.4660 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 1.929923 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): -1.551000 53.78800 ymin,ymax (A): -22.78400 22.90800 zmin,zma (A): 8.827000 53.88100 x,y,z range (A): 55.33900 45.69200 45.05400 scale (grids/A): 1.929923 object centre (A): 26.11850 6.1999321E-02 31.35400 number of atom coordinates read : 2380 total number of charged atoms : 2232 net assigned charge : 6.425008 assigned positive charge : 360.7343 centred at (gu) : 86.06596 91.13577 90.31031 assigned negative charge : -354.3098 centred at (gu) : 86.05116 90.86761 89.65475 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19949 grid for indexing accessible points = 1.400000 m= 26318 mr = 50157 m= 4099 mr = 19714 m= 264 mr = 2488 m= 6 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 29624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17583 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) : 0.6433076 object centre at (A) : 26.11850 6.1999321E-02 31.35400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9351363E-02 4.4745848E-02 midg,1,midg; midg,igrid,midg -2.8596269E-03 9.1963625E-03 1,midg,midg; igrid,midg,midg 1.8323256E-02 2.6221469E-02 gauss-seidel spectral radius is 0.9986473 estimated iterations to convergence 215 setup time was (sec) 0.5800000 now iterating at: 07:54:28 rms-change max change #iterations 4.161251 173.6741 at 10iterations 1.953473 80.59655 at 20iterations 0.9260804 32.24573 at 30iterations 0.4372701 16.46549 at 40iterations 0.2054646 6.750526 at 50iterations 9.6673600E-02 2.986305 at 60iterations 4.5471437E-02 1.525150 at 70iterations 2.1402340E-02 0.6458198 at 80iterations 1.0106045E-02 0.3730164 at 90iterations 4.7725239E-03 0.1481285 at 100iterations 2.2439389E-03 7.4451447E-02 at 110iterations 1.0630648E-03 3.5217285E-02 at 120iterations finished qdiffx linear iterations at : 07:54:35 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.0630648E-03 3.5217285E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 07:54:35 7.746u 0.183s 0:08.30 95.4% 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 Tue Oct 11 2011 at 07:54:35 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: THS 97 has a net charge of 0.4660 !!! WARNING: HIR 99 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.894884 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): -1.551000 53.78800 ymin,ymax (A): -22.78400 22.90800 zmin,zma (A): 8.827000 53.88100 x,y,z range (A): 55.33900 45.69200 45.05400 scale (grids/A): 2.894884 object centre (A): 26.11850 6.1999321E-02 31.35400 number of atom coordinates read : 2380 total number of charged atoms : 2232 net assigned charge : 6.425008 assigned positive charge : 360.7343 centred at (gu) : 84.09887 91.70354 90.46541 assigned negative charge : -354.3098 centred at (gu) : 84.07684 91.30148 89.48212 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 165032 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19949 grid for indexing accessible points = 1.400000 m= 85270 mr = 121170 m= 30982 mr = 70765 m= 7257 mr = 24901 m= 1077 mr = 5356 m= 65 mr = 697 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 66773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 17854 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) : 1.929923 object centre at (A) : 26.11850 6.1999321E-02 31.35400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2892319 0.4559607 midg,1,midg; midg,igrid,midg -3.2313861E-02 -6.6102287E-03 1,midg,midg; igrid,midg,midg 0.1220618 0.1694129 gauss-seidel spectral radius is 0.9992534 estimated iterations to convergence 289 setup time was (sec) 1.160000 now iterating at: 07:54:37 rms-change max change #iterations 9.650753 484.0676 at 10iterations 5.623426 158.8488 at 20iterations 3.258333 66.50033 at 30iterations 1.883885 36.61946 at 40iterations 1.088767 20.60990 at 50iterations 0.6248316 11.30376 at 60iterations 0.3600746 7.113173 at 70iterations 0.2066138 4.036499 at 80iterations 0.1187912 2.174599 at 90iterations 6.8133466E-02 1.198010 at 100iterations 3.9153453E-02 0.7376866 at 110iterations 2.2479447E-02 0.3844242 at 120iterations 1.2921123E-02 0.2493210 at 130iterations 7.4324496E-03 0.1453743 at 140iterations 4.2750523E-03 8.1340790E-02 at 150iterations 2.4745460E-03 4.4563293E-02 at 160iterations 1.4444456E-03 2.5026321E-02 at 170iterations 8.4944267E-04 1.6593933E-02 at 180iterations finished qdiffx linear iterations at : 07:54:48 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 8.4944267E-04 1.6593933E-02 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.41000 DelPhi exited at 07:54:48 12.417u 0.202s 0:13.00 97.0% 0+0k 0+0io 0pf+0w