Sun Oct 9 07:30:48 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 07:30:48 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2406 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5903912 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): -6.732000 52.97500 ymin,ymax (A): 20.04900 70.63300 zmin,zma (A): 51.21000 111.5090 x,y,z range (A): 59.70700 50.58400 60.29900 scale (grids/A): 0.5903912 object centre (A): 23.12150 45.34100 81.35950 number of atom coordinates read : 2406 total number of charged atoms : 2261 net assigned charge : -12.49998 assigned positive charge : 360.6441 centred at (gu) : 88.81817 90.84383 87.10468 assigned negative charge : -373.1444 centred at (gu) : 88.76519 91.22755 86.93249 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5576 nv = 96 ne = 84 npr = 47208 no. pairs analyzed = 47208 no. exposed pairs = 3406 no. arc points = 24514 no. surface atoms = 1138 nbur = 1268 mkacc time = 9.9999994E-02 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 = 1.456000 m= 259 mr = 2634 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3000000 number of dielectric boundary points 3185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2405 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6907 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5823879E-08 3.1466293E-10 midg,1,midg; midg,igrid,midg 4.7350297E-09 -1.6819323E-08 1,midg,midg; igrid,midg,midg -6.4462471E-09 -1.7298686E-09 gauss-seidel spectral radius is 0.9851510 estimated iterations to convergence 67 setup time was (sec) 0.5200000 now iterating at: 07:30:48 rms-change max change #iterations 9.5466778E-02 18.80889 at 10iterations 7.6655084E-03 1.406845 at 20iterations 6.1777752E-04 0.1070938 at 30iterations 5.0626986E-05 1.0904312E-02 at 40iterations 4.1409444E-06 6.0272217E-04 at 50iterations finished qdiffx linear iterations at : 07:30:51 total time elapsed so far: 2.970000 # loops : 50 mean,max change (kT/e) : 4.1409444E-06 6.0272217E-04 energy calculations done at 2.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 07:30:51 3.166u 0.145s 0:03.64 90.6% 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 07:30:51 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2406 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: 1.771174 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): -6.732000 52.97500 ymin,ymax (A): 20.04900 70.63300 zmin,zma (A): 51.21000 111.5090 x,y,z range (A): 59.70700 50.58400 60.29900 scale (grids/A): 1.771174 object centre (A): 23.12150 45.34100 81.35950 number of atom coordinates read : 2406 total number of charged atoms : 2261 net assigned charge : -12.49998 assigned positive charge : 360.6441 centred at (gu) : 86.45404 92.53101 81.31358 assigned negative charge : -373.1444 centred at (gu) : 86.29547 93.68243 80.79708 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 59444 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24514 grid for indexing accessible points = 1.400000 m= 18734 mr = 36807 m= 2347 mr = 12776 m= 102 mr = 1343 m= 0 mr = 29 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1008 time to turn everything in is 0.4500000 number of dielectric boundary points 29672 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 17594 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) : 0.5903912 object centre at (A) : 23.12150 45.34100 81.35950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0442467E-02 1.1426261E-02 midg,1,midg; midg,igrid,midg 4.7806432E-04 -4.8291076E-02 1,midg,midg; igrid,midg,midg -3.1258713E-02 -2.4205469E-02 gauss-seidel spectral radius is 0.9984019 estimated iterations to convergence 198 setup time was (sec) 0.7200000 now iterating at: 07:30:52 rms-change max change #iterations 3.550951 176.3463 at 10iterations 1.551753 81.32874 at 20iterations 0.6837886 25.69620 at 30iterations 0.2989684 11.07915 at 40iterations 0.1310190 4.750955 at 50iterations 5.7514641E-02 2.081263 at 60iterations 2.5224607E-02 0.9231071 at 70iterations 1.1074150E-02 0.3979034 at 80iterations 4.8673921E-03 0.1832561 at 90iterations 2.1299787E-03 7.6620370E-02 at 100iterations 9.3238743E-04 3.2361984E-02 at 110iterations 4.1149248E-04 1.5127182E-02 at 120iterations finished qdiffx linear iterations at : 07:30:59 total time elapsed so far: 7.130000 # loops : 120 mean,max change (kT/e) : 4.1149248E-04 1.5127182E-02 energy calculations done at 7.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.300000 DelPhi exited at 07:30:59 7.302u 0.196s 0:07.75 96.6% 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 07:30:59 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2406 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: 2.656760 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): -6.732000 52.97500 ymin,ymax (A): 20.04900 70.63300 zmin,zma (A): 51.21000 111.5090 x,y,z range (A): 59.70700 50.58400 60.29900 scale (grids/A): 2.656760 object centre (A): 23.12150 45.34100 81.35950 number of atom coordinates read : 2406 total number of charged atoms : 2261 net assigned charge : -12.49998 assigned positive charge : 360.6441 centred at (gu) : 84.68097 93.79652 76.97029 assigned negative charge : -373.1444 centred at (gu) : 84.44312 95.52355 76.19559 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 137303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24514 grid for indexing accessible points = 1.400000 m= 62133 mr = 90385 m= 20083 mr = 48193 m= 3926 mr = 15311 m= 422 mr = 2764 m= 18 mr = 251 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 3551 time to turn everything in is 1.020000 number of dielectric boundary points 66975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 18082 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) : 1.771174 object centre at (A) : 23.12150 45.34100 81.35950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3473511 0.1721968 midg,1,midg; midg,igrid,midg 3.2806076E-02 -0.5362571 1,midg,midg; igrid,midg,midg -0.1620308 -0.3469808 gauss-seidel spectral radius is 0.9992038 estimated iterations to convergence 280 setup time was (sec) 1.300000 now iterating at: 07:31:01 rms-change max change #iterations 8.890704 286.7829 at 10iterations 5.133371 156.2880 at 20iterations 2.913197 83.50516 at 30iterations 1.657169 38.16658 at 40iterations 0.9402693 24.11046 at 50iterations 0.5299388 12.87791 at 60iterations 0.3001239 6.158286 at 70iterations 0.1691274 3.621834 at 80iterations 9.5436335E-02 1.916414 at 90iterations 5.3639807E-02 1.309307 at 100iterations 3.0187683E-02 0.6337204 at 110iterations 1.6962657E-02 0.3565369 at 120iterations 9.5563838E-03 0.2031211 at 130iterations 5.3593898E-03 0.1372623 at 140iterations 3.0137259E-03 6.1120987E-02 at 150iterations 1.6953376E-03 3.6319733E-02 at 160iterations 9.4845227E-04 1.9792557E-02 at 170iterations 5.3286989E-04 1.0662556E-02 at 180iterations finished qdiffx linear iterations at : 07:31:10 total time elapsed so far: 10.76000 # loops : 180 mean,max change (kT/e) : 5.3286989E-04 1.0662556E-02 energy calculations done at 10.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.93000 DelPhi exited at 07:31:11 10.933u 0.227s 0:11.42 97.6% 0+0k 0+0io 0pf+0w