Sun Oct 9 06:39:45 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 Sun Oct 9 2011 at 06:39:45 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2015 !!! WARNING: GLM 32 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6587957 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): 2.874000 46.28200 ymin,ymax (A): 8.985001 54.72600 zmin,zma (A): 1.200000 55.23800 x,y,z range (A): 43.40800 45.74100 54.03800 scale (grids/A): 0.6587957 object centre (A): 24.57800 31.85550 28.21900 number of atom coordinates read : 2015 total number of charged atoms : 1870 net assigned charge : 2.406015 assigned positive charge : 299.9879 centred at (gu) : 89.03998 89.23409 88.70497 assigned negative charge : -297.5821 centred at (gu) : 89.00401 89.36967 88.61715 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5841 nv = 96 ne = 84 npr = 41030 no. pairs analyzed = 41030 no. exposed pairs = 2679 no. arc points = 18579 no. surface atoms = 899 nbur = 1116 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 334 mr = 3006 m= 0 mr = 42 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3127 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1759 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6742 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.3651682E-09 1.4338433E-08 midg,1,midg; midg,igrid,midg 3.0077114E-08 -1.2000803E-08 1,midg,midg; igrid,midg,midg 7.7989643E-10 9.2384731E-09 gauss-seidel spectral radius is 0.9880065 estimated iterations to convergence 75 setup time was (sec) 0.4600000 now iterating at: 06:39:45 rms-change max change #iterations 0.1445589 26.33809 at 10iterations 1.5192797E-02 2.021510 at 20iterations 1.5953509E-03 0.2367549 at 30iterations 1.6686898E-04 2.6817322E-02 at 40iterations 1.7654684E-05 3.2577515E-03 at 50iterations finished qdiffx linear iterations at : 06:39:48 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.7654684E-05 3.2577515E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 06:39:48 3.090u 0.140s 0:03.57 90.4% 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 Sun Oct 9 2011 at 06:39:48 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2015 !!! WARNING: GLM 32 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.976387 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): 2.874000 46.28200 ymin,ymax (A): 8.985001 54.72600 zmin,zma (A): 1.200000 55.23800 x,y,z range (A): 43.40800 45.74100 54.03800 scale (grids/A): 1.976387 object centre (A): 24.57800 31.85550 28.21900 number of atom coordinates read : 2015 total number of charged atoms : 1870 net assigned charge : 2.406015 assigned positive charge : 299.9879 centred at (gu) : 87.11998 87.70235 86.11495 assigned negative charge : -297.5821 centred at (gu) : 87.01197 88.10913 85.85146 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 61516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18579 grid for indexing accessible points = 1.400000 m= 22427 mr = 40814 m= 3914 mr = 16254 m= 271 mr = 2428 m= 6 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 211 time to turn everything in is 0.4600000 number of dielectric boundary points 28540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 14778 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) : 0.6587957 object centre at (A) : 24.57800 31.85550 28.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7219183E-02 -3.8753261E-03 midg,1,midg; midg,igrid,midg 2.4315836E-02 -1.3343680E-02 1,midg,midg; igrid,midg,midg 8.9467363E-03 2.8214183E-02 gauss-seidel spectral radius is 0.9986717 estimated iterations to convergence 217 setup time was (sec) 0.7200000 now iterating at: 06:39:49 rms-change max change #iterations 3.952700 209.0632 at 10iterations 1.862391 70.89149 at 20iterations 0.8784766 33.89017 at 30iterations 0.4131759 15.06184 at 40iterations 0.1959809 6.719182 at 50iterations 9.2271879E-02 2.993286 at 60iterations 4.3679878E-02 1.692454 at 70iterations 2.0629996E-02 0.8533630 at 80iterations 9.7529227E-03 0.3482513 at 90iterations 4.6063480E-03 0.1529617 at 100iterations 2.1725928E-03 7.6377869E-02 at 110iterations 1.0321700E-03 3.3576965E-02 at 120iterations finished qdiffx linear iterations at : 06:39:55 total time elapsed so far: 6.680000 # loops : 120 mean,max change (kT/e) : 1.0321700E-03 3.3576965E-02 energy calculations done at 6.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.850000 DelPhi exited at 06:39:56 6.854u 0.166s 0:07.29 96.1% 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 Sun Oct 9 2011 at 06:39:56 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2015 !!! WARNING: GLM 32 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.964581 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): 2.874000 46.28200 ymin,ymax (A): 8.985001 54.72600 zmin,zma (A): 1.200000 55.23800 x,y,z range (A): 43.40800 45.74100 54.03800 scale (grids/A): 2.964581 object centre (A): 24.57800 31.85550 28.21900 number of atom coordinates read : 2015 total number of charged atoms : 1870 net assigned charge : 2.406015 assigned positive charge : 299.9879 centred at (gu) : 85.67985 86.55354 84.17239 assigned negative charge : -297.5821 centred at (gu) : 85.51802 87.16373 83.77712 start vw surface at 0.1300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 141550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18579 grid for indexing accessible points = 1.400000 m= 70939 mr = 98860 m= 27250 mr = 57016 m= 7124 mr = 21730 m= 1121 mr = 5271 m= 104 mr = 723 m= 1 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 650 time to turn everything in is 1.120000 number of dielectric boundary points 64428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 14956 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) : 1.976387 object centre at (A) : 24.57800 31.85550 28.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8599399 -4.4101290E-02 midg,1,midg; midg,igrid,midg 0.2895100 -0.1146183 1,midg,midg; igrid,midg,midg 2.2994023E-02 0.2873387 gauss-seidel spectral radius is 0.9992639 estimated iterations to convergence 291 setup time was (sec) 1.390000 now iterating at: 06:39:57 rms-change max change #iterations 9.207794 356.5886 at 10iterations 5.320566 111.9480 at 20iterations 3.060197 63.75015 at 30iterations 1.769167 35.12851 at 40iterations 1.017887 19.60521 at 50iterations 0.5851614 11.64377 at 60iterations 0.3363307 6.543418 at 70iterations 0.1935203 3.982432 at 80iterations 0.1110329 2.200029 at 90iterations 6.3619658E-02 1.254066 at 100iterations 3.6631070E-02 0.8120728 at 110iterations 2.0989275E-02 0.4504833 at 120iterations 1.2058096E-02 0.2222242 at 130iterations 6.9149509E-03 0.1306839 at 140iterations 3.9786282E-03 7.5669289E-02 at 150iterations 2.2825573E-03 4.9434662E-02 at 160iterations 1.3110522E-03 2.5016785E-02 at 170iterations 7.5222674E-04 1.4484406E-02 at 180iterations finished qdiffx linear iterations at : 06:40:06 total time elapsed so far: 10.71000 # loops : 180 mean,max change (kT/e) : 7.5222674E-04 1.4484406E-02 energy calculations done at 10.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.88000 DelPhi exited at 06:40:07 10.887u 0.189s 0:11.34 97.5% 0+0k 0+0io 0pf+0w