Sat Oct 15 15:35:52 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 Sat Oct 15 2011 at 15:35:55 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 = 2113 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: 0.7081759 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): 17.03200 62.45300 ymin,ymax (A): -3.521000 33.49900 zmin,zma (A): 19.83400 70.10400 x,y,z range (A): 45.42101 37.02000 50.27000 scale (grids/A): 0.7081759 object centre (A): 39.74250 14.98900 44.96900 number of atom coordinates read : 2113 total number of charged atoms : 1985 net assigned charge : 6.500009 assigned positive charge : 322.5209 centred at (gu) : 91.09187 89.51307 89.36485 assigned negative charge : -316.0211 centred at (gu) : 91.23798 89.54900 89.30074 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7047 nv = 96 ne = 84 npr = 42660 no. pairs analyzed = 42660 no. exposed pairs = 2524 no. arc points = 17088 no. surface atoms = 860 nbur = 1253 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 4062 m= 7 mr = 83 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 0.2600000 number of dielectric boundary points 3346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1619 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7956 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6831259E-08 7.8990531E-08 midg,1,midg; midg,igrid,midg 8.2353999E-08 3.5244454E-08 1,midg,midg; igrid,midg,midg 1.0530078E-07 -2.3982357E-08 gauss-seidel spectral radius is 0.9896053 estimated iterations to convergence 80 setup time was (sec) 0.5600000 now iterating at: 15:35:56 rms-change max change #iterations 0.2043733 27.55991 at 10iterations 2.5398081E-02 3.770697 at 20iterations 3.2827293E-03 0.4143143 at 30iterations 4.6120692E-04 6.3316345E-02 at 40iterations 8.8928660E-05 1.2985229E-02 at 50iterations finished qdiffx linear iterations at : 15:36:07 total time elapsed so far: 5.140000 # loops : 50 mean,max change (kT/e) : 8.8928660E-05 1.2985229E-02 energy calculations done at 5.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.300000 DelPhi exited at 15:36:09 5.307u 0.501s 0:14.63 39.6% 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 Sat Oct 15 2011 at 15:36:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2113 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: 2.124528 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): 17.03200 62.45300 ymin,ymax (A): -3.521000 33.49900 zmin,zma (A): 19.83400 70.10400 x,y,z range (A): 45.42101 37.02000 50.27000 scale (grids/A): 2.124528 object centre (A): 39.74250 14.98900 44.96900 number of atom coordinates read : 2113 total number of charged atoms : 1985 net assigned charge : 6.500009 assigned positive charge : 322.5209 centred at (gu) : 93.27551 88.53928 88.09451 assigned negative charge : -316.0211 centred at (gu) : 93.71384 88.64723 87.90226 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75189 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17088 grid for indexing accessible points = 1.400000 m= 30153 mr = 53737 m= 5923 mr = 22970 m= 550 mr = 3991 m= 12 mr = 286 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 30843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 82 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15759 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) : 0.7081759 object centre at (A) : 39.74250 14.98900 44.96900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8649816E-02 5.7511900E-02 midg,1,midg; midg,igrid,midg 3.5631552E-02 9.3461704E-03 1,midg,midg; igrid,midg,midg 2.6953673E-02 9.1762543E-03 gauss-seidel spectral radius is 0.9988309 estimated iterations to convergence 232 setup time was (sec) 1.020000 now iterating at: 15:36:14 rms-change max change #iterations 4.652262 227.8780 at 10iterations 2.298743 79.66060 at 20iterations 1.139121 37.49663 at 30iterations 0.5667511 16.87577 at 40iterations 0.2819462 7.870872 at 50iterations 0.1396843 4.194632 at 60iterations 6.9368355E-02 2.102058 at 70iterations 3.4504734E-02 1.010881 at 80iterations 1.7198775E-02 0.4811391 at 90iterations 8.5587408E-03 0.2678223 at 100iterations 4.2619002E-03 0.1256981 at 110iterations 2.1530730E-03 6.8435669E-02 at 120iterations finished qdiffx linear iterations at : 15:36:41 total time elapsed so far: 13.00000 # loops : 120 mean,max change (kT/e) : 2.1530730E-03 6.8435669E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 15:36:42 13.182u 0.511s 0:32.01 42.7% 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 Sat Oct 15 2011 at 15:36:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2113 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: 3.186792 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): 17.03200 62.45300 ymin,ymax (A): -3.521000 33.49900 zmin,zma (A): 19.83400 70.10400 x,y,z range (A): 45.42101 37.02000 50.27000 scale (grids/A): 3.186792 object centre (A): 39.74250 14.98900 44.96900 number of atom coordinates read : 2113 total number of charged atoms : 1985 net assigned charge : 6.500009 assigned positive charge : 322.5209 centred at (gu) : 94.91329 87.80886 87.14181 assigned negative charge : -316.0211 centred at (gu) : 95.57077 87.97075 86.85349 start vw surface at 0.1100000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 173373 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17088 grid for indexing accessible points = 1.400000 m= 94107 mr = 129366 m= 38306 mr = 78514 m= 11133 mr = 31511 m= 2234 mr = 8626 m= 255 mr = 1651 m= 8 mr = 142 m= 0 mr = 2 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.030000 number of dielectric boundary points 69604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.190000 number of grid points assigned charge 15880 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) : 2.124528 object centre at (A) : 39.74250 14.98900 44.96900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3441065 0.4252585 midg,1,midg; midg,igrid,midg 0.3141135 6.3554294E-02 1,midg,midg; igrid,midg,midg 0.2311040 0.2689200 gauss-seidel spectral radius is 0.9992950 estimated iterations to convergence 297 setup time was (sec) 2.420000 now iterating at: 15:36:48 rms-change max change #iterations 10.34282 354.5570 at 10iterations 6.115674 137.5059 at 20iterations 3.601825 75.74893 at 30iterations 2.121256 42.12207 at 40iterations 1.246551 24.52691 at 50iterations 0.7332678 15.48627 at 60iterations 0.4291051 7.459652 at 70iterations 0.2512966 4.428913 at 80iterations 0.1472155 2.649357 at 90iterations 8.6086787E-02 1.517916 at 100iterations 5.0426230E-02 0.9418118 at 110iterations 2.9638477E-02 0.5168457 at 120iterations 1.7445309E-02 0.3188529 at 130iterations 1.0354327E-02 0.1804886 at 140iterations 6.2519521E-03 0.1086807 at 150iterations 3.8348963E-03 7.2282791E-02 at 160iterations 2.4527824E-03 4.6669960E-02 at 170iterations 1.6453207E-03 3.1711578E-02 at 180iterations finished qdiffx linear iterations at : 15:37:31 total time elapsed so far: 21.90000 # loops : 180 mean,max change (kT/e) : 1.6453207E-03 3.1711578E-02 energy calculations done at 21.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.07000 DelPhi exited at 15:37:32 22.079u 0.558s 0:49.44 45.7% 0+0k 0+0io 0pf+0w