Sun Oct 9 16:43:36 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 16:43:36 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2386 !!! WARNING: ASL 40 has a net charge of -0.1000 !!! WARNING: GLM 46 has a net charge of -0.0940 !!! WARNING: GLM 118 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: 0.6631769 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): -53.15500 -8.525000 ymin,ymax (A): 4.102000 54.90500 zmin,zma (A): -25.57000 28.11100 x,y,z range (A): 44.63000 50.80300 53.68100 scale (grids/A): 0.6631769 object centre (A): -30.84000 29.50350 1.270500 number of atom coordinates read : 2386 total number of charged atoms : 2270 net assigned charge : 0.7120094 assigned positive charge : 354.0291 centred at (gu) : 90.32442 88.86828 88.67389 assigned negative charge : -353.3179 centred at (gu) : 90.40536 88.94850 88.78554 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7231 nv = 96 ne = 84 npr = 47701 no. pairs analyzed = 47701 no. exposed pairs = 2995 no. arc points = 21292 no. surface atoms = 1016 nbur = 1370 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 419 mr = 3943 m= 2 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.1900000 number of dielectric boundary points 3638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2046 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8387 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0502285E-08 -1.5483296E-08 midg,1,midg; midg,igrid,midg 2.1628299E-08 -1.1202484E-08 1,midg,midg; igrid,midg,midg 1.6031002E-08 -1.5409420E-08 gauss-seidel spectral radius is 0.9882000 estimated iterations to convergence 75 setup time was (sec) 0.3700000 now iterating at: 16:43:36 rms-change max change #iterations 0.1603233 22.31177 at 10iterations 1.7204136E-02 2.680231 at 20iterations 1.8920382E-03 0.2954197 at 30iterations 2.4978627E-04 3.2882690E-02 at 40iterations 5.3758460E-05 7.0114136E-03 at 50iterations finished qdiffx linear iterations at : 16:43:39 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 5.3758460E-05 7.0114136E-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) 3.380000 DelPhi exited at 16:43:40 3.384u 0.178s 0:03.87 91.7% 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 Sun Oct 9 2011 at 16:43:40 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2386 !!! WARNING: ASL 40 has a net charge of -0.1000 !!! WARNING: GLM 46 has a net charge of -0.0940 !!! WARNING: GLM 118 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: 1.989531 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): -53.15500 -8.525000 ymin,ymax (A): 4.102000 54.90500 zmin,zma (A): -25.57000 28.11100 x,y,z range (A): 44.63000 50.80300 53.68100 scale (grids/A): 1.989531 object centre (A): -30.84000 29.50350 1.270500 number of atom coordinates read : 2386 total number of charged atoms : 2270 net assigned charge : 0.7120094 assigned positive charge : 354.0291 centred at (gu) : 90.97253 86.60438 86.02084 assigned negative charge : -353.3179 centred at (gu) : 91.21590 86.84536 86.35660 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21292 grid for indexing accessible points = 1.400000 m= 29023 mr = 53451 m= 5564 mr = 21572 m= 478 mr = 3581 m= 4 mr = 230 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.3900000 number of dielectric boundary points 33597 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 138 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 17971 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) : 0.6631769 object centre at (A) : -30.84000 29.50350 1.270500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2882158E-02 2.2340303E-03 midg,1,midg; midg,igrid,midg -2.1596192E-03 -4.3251291E-03 1,midg,midg; igrid,midg,midg 1.4760598E-02 -2.6870802E-02 gauss-seidel spectral radius is 0.9987315 estimated iterations to convergence 222 setup time was (sec) 0.6100000 now iterating at: 16:43:40 rms-change max change #iterations 4.448195 190.0833 at 10iterations 2.145372 74.42229 at 20iterations 1.031917 31.69743 at 30iterations 0.4969360 16.66851 at 40iterations 0.2410412 8.187028 at 50iterations 0.1159355 3.673447 at 60iterations 5.5700779E-02 1.737183 at 70iterations 2.6946994E-02 0.8251400 at 80iterations 1.2984956E-02 0.3744755 at 90iterations 6.2679821E-03 0.1830063 at 100iterations 3.0368429E-03 0.1117439 at 110iterations 1.4634480E-03 4.6113014E-02 at 120iterations finished qdiffx linear iterations at : 16:43:47 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 1.4634480E-03 4.6113014E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 16:43:48 7.888u 0.194s 0:08.40 96.0% 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 16:43:48 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2386 !!! WARNING: ASL 40 has a net charge of -0.1000 !!! WARNING: GLM 46 has a net charge of -0.0940 !!! WARNING: GLM 118 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: 2.984296 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): -53.15500 -8.525000 ymin,ymax (A): 4.102000 54.90500 zmin,zma (A): -25.57000 28.11100 x,y,z range (A): 44.63000 50.80300 53.68100 scale (grids/A): 2.984296 object centre (A): -30.84000 29.50350 1.270500 number of atom coordinates read : 2386 total number of charged atoms : 2270 net assigned charge : 0.7120094 assigned positive charge : 354.0291 centred at (gu) : 91.45875 84.90635 84.03125 assigned negative charge : -353.3179 centred at (gu) : 91.82383 85.26817 84.53496 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 178766 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21292 grid for indexing accessible points = 1.400000 m= 91241 mr = 129707 m= 36138 mr = 74663 m= 10380 mr = 29207 m= 1930 mr = 7885 m= 195 mr = 1366 m= 3 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 178 time to turn everything in is 1.020000 number of dielectric boundary points 75725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 18160 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) : 1.989531 object centre at (A) : -30.84000 29.50350 1.270500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2017197 0.1879633 midg,1,midg; midg,igrid,midg -8.4415182E-02 2.7333913E-02 1,midg,midg; igrid,midg,midg 0.1113987 -0.3574995 gauss-seidel spectral radius is 0.9992827 estimated iterations to convergence 295 setup time was (sec) 1.260000 now iterating at: 16:43:49 rms-change max change #iterations 10.25949 492.1323 at 10iterations 6.018937 144.1482 at 20iterations 3.520772 71.04796 at 30iterations 2.062355 41.69512 at 40iterations 1.203721 24.43572 at 50iterations 0.7015573 12.35144 at 60iterations 0.4084886 7.517235 at 70iterations 0.2375444 4.331308 at 80iterations 0.1381920 2.384579 at 90iterations 8.0193788E-02 1.364307 at 100iterations 4.6607543E-02 0.8690505 at 110iterations 2.7097773E-02 0.4742088 at 120iterations 1.5718922E-02 0.2813950 at 130iterations 9.1129886E-03 0.1585822 at 140iterations 5.3001083E-03 9.2198610E-02 at 150iterations 3.0856084E-03 5.9570313E-02 at 160iterations 1.7986317E-03 3.0622303E-02 at 170iterations 1.0553963E-03 1.8415451E-02 at 180iterations finished qdiffx linear iterations at : 16:44:01 total time elapsed so far: 12.72000 # loops : 180 mean,max change (kT/e) : 1.0553963E-03 1.8415451E-02 energy calculations done at 12.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.87000 DelPhi exited at 16:44:01 12.870u 0.185s 0:13.31 98.0% 0+0k 0+0io 0pf+0w