Sun Oct 9 23:54:40 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 Sun Oct 9 2011 at 23:54:40 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 = 2982 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: 0.5633090 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): -28.14300 25.70600 ymin,ymax (A): 15.23700 72.65900 zmin,zma (A): -27.03600 36.16200 x,y,z range (A): 53.84900 57.42200 63.19800 scale (grids/A): 0.5633090 object centre (A): -1.218499 43.94800 4.563002 number of atom coordinates read : 2982 total number of charged atoms : 2841 net assigned charge : 3.000009 assigned positive charge : 457.1344 centred at (gu) : 89.97240 88.32743 89.81260 assigned negative charge : -454.1355 centred at (gu) : 89.95132 88.22331 89.83173 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6108 nv = 96 ne = 84 npr = 57777 no. pairs analyzed = 57777 no. exposed pairs = 4013 no. arc points = 29120 no. surface atoms = 1334 nbur = 1648 mkacc time = 9.0000004E-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 = 1.512000 m= 275 mr = 2966 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.2200000 number of dielectric boundary points 3410 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2946 ## 387 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8015 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5533146E-10 1.3599820E-10 midg,1,midg; midg,igrid,midg -1.4521302E-09 1.1306339E-09 1,midg,midg; igrid,midg,midg 1.1746369E-10 6.4697592E-10 gauss-seidel spectral radius is 0.9837488 estimated iterations to convergence 65 setup time was (sec) 0.4300000 now iterating at: 23:54:41 rms-change max change #iterations 8.5679188E-02 14.49389 at 10iterations 6.0382239E-03 0.9918060 at 20iterations 4.3087589E-04 8.5670471E-02 at 30iterations 3.1561569E-05 5.5732727E-03 at 40iterations 2.3310379E-06 3.7384033E-04 at 50iterations finished qdiffx linear iterations at : 23:54:44 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 2.3310379E-06 3.7384033E-04 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 23:54:45 3.739u 0.207s 0:04.35 90.3% 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 Sun Oct 9 2011 at 23:54:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2982 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: 1.689927 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): -28.14300 25.70600 ymin,ymax (A): 15.23700 72.65900 zmin,zma (A): -27.03600 36.16200 x,y,z range (A): 53.84900 57.42200 63.19800 scale (grids/A): 1.689927 object centre (A): -1.218499 43.94800 4.563002 number of atom coordinates read : 2982 total number of charged atoms : 2841 net assigned charge : 3.000009 assigned positive charge : 457.1344 centred at (gu) : 89.91618 84.98178 89.43687 assigned negative charge : -454.1355 centred at (gu) : 89.85375 84.66971 89.49509 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 67075 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29120 grid for indexing accessible points = 1.400000 m= 20385 mr = 43221 m= 2316 mr = 13875 m= 64 mr = 1111 m= 0 mr = 6 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 694 time to turn everything in is 0.3600000 number of dielectric boundary points 31627 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 320 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21884 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) : 0.5633090 object centre at (A) : -1.218499 43.94800 4.563002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8765806E-03 -4.3594954E-03 midg,1,midg; midg,igrid,midg -3.0776269E-03 1.6077574E-02 1,midg,midg; igrid,midg,midg 1.9117143E-03 7.4484485E-04 gauss-seidel spectral radius is 0.9983223 estimated iterations to convergence 194 setup time was (sec) 0.5900000 now iterating at: 23:54:46 rms-change max change #iterations 3.614961 176.8968 at 10iterations 1.540881 58.73238 at 20iterations 0.6636644 23.50425 at 30iterations 0.2852000 11.21541 at 40iterations 0.1224339 4.346249 at 50iterations 5.2700311E-02 1.799678 at 60iterations 2.2719955E-02 0.7896671 at 70iterations 9.7746542E-03 0.3503418 at 80iterations 4.2092260E-03 0.1382217 at 90iterations 1.8188907E-03 7.0578575E-02 at 100iterations 7.8072591E-04 2.8223515E-02 at 110iterations 3.3705821E-04 1.1587143E-02 at 120iterations finished qdiffx linear iterations at : 23:54:54 total time elapsed so far: 8.340000 # loops : 120 mean,max change (kT/e) : 3.3705821E-04 1.1587143E-02 energy calculations done at 8.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.490000 DelPhi exited at 23:54:55 8.497u 0.307s 0:09.84 89.3% 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 Sun Oct 9 2011 at 23:54:55 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 = 2982 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: 2.534890 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): -28.14300 25.70600 ymin,ymax (A): 15.23700 72.65900 zmin,zma (A): -27.03600 36.16200 x,y,z range (A): 53.84900 57.42200 63.19800 scale (grids/A): 2.534890 object centre (A): -1.218499 43.94800 4.563002 number of atom coordinates read : 2982 total number of charged atoms : 2841 net assigned charge : 3.000009 assigned positive charge : 457.1344 centred at (gu) : 89.87415 82.47246 89.15509 assigned negative charge : -454.1355 centred at (gu) : 89.78053 82.00462 89.24267 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 155609 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29120 grid for indexing accessible points = 1.400000 m= 69332 mr = 106209 m= 20408 mr = 53894 m= 3578 mr = 15248 m= 323 mr = 2360 m= 3 mr = 151 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 2351 time to turn everything in is 0.8400000 number of dielectric boundary points 71392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 22710 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) : 1.689927 object centre at (A) : -1.218499 43.94800 4.563002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7983247E-02 -4.0117148E-02 midg,1,midg; midg,igrid,midg 1.6670000E-02 0.2253628 1,midg,midg; igrid,midg,midg 3.9739780E-02 -1.0674552E-02 gauss-seidel spectral radius is 0.9991861 estimated iterations to convergence 277 setup time was (sec) 1.090000 now iterating at: 23:54:56 rms-change max change #iterations 9.197524 319.9694 at 10iterations 5.252423 139.0634 at 20iterations 2.978641 66.61365 at 30iterations 1.685473 38.46831 at 40iterations 0.9499234 23.66352 at 50iterations 0.5361237 12.13698 at 60iterations 0.3009432 6.230362 at 70iterations 0.1689979 3.406793 at 80iterations 9.4803356E-02 2.093812 at 90iterations 5.3004771E-02 1.038180 at 100iterations 2.9714001E-02 0.5479128 at 110iterations 1.6591856E-02 0.3458834 at 120iterations 9.2953900E-03 0.2237868 at 130iterations 5.1945630E-03 0.1131592 at 140iterations 2.9106014E-03 6.2896729E-02 at 150iterations 1.6252439E-03 3.0924737E-02 at 160iterations 9.0846367E-04 1.8579960E-02 at 170iterations 5.0733943E-04 1.0026932E-02 at 180iterations finished qdiffx linear iterations at : 23:55:09 total time elapsed so far: 13.57000 # loops : 180 mean,max change (kT/e) : 5.0733943E-04 1.0026932E-02 energy calculations done at 13.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.70000 DelPhi exited at 23:55:09 13.704u 0.253s 0:14.55 95.8% 0+0k 0+0io 0pf+0w