Sat Oct 8 11:34:35 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 8 2011 at 11:34:35 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 = 4362 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: 0.5355155 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): 59.82900 115.3300 ymin,ymax (A): 19.66500 81.52000 zmin,zma (A): -10.28500 56.19300 x,y,z range (A): 55.50100 61.85500 66.47800 scale (grids/A): 0.5355155 object centre (A): 87.57950 50.59250 22.95400 number of atom coordinates read : 4362 total number of charged atoms : 4203 net assigned charge : -0.9999546 assigned positive charge : 654.5993 centred at (gu) : 89.45560 90.05664 90.12487 assigned negative charge : -655.6025 centred at (gu) : 89.63944 89.99479 89.98507 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7805 nv = 96 ne = 84 npr = 91997 no. pairs analyzed = 91997 no. exposed pairs = 5012 no. arc points = 33896 no. surface atoms = 1697 nbur = 2665 mkacc time = 0.1600000 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 = 1.624000 m= 307 mr = 4352 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 88 time to turn everything in is 0.3000000 number of dielectric boundary points 3740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3514 ## 463 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 10539 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.5386943E-10 8.8375635E-10 midg,1,midg; midg,igrid,midg -4.5177653E-10 3.6111625E-10 1,midg,midg; igrid,midg,midg 1.3044578E-09 -1.1199139E-09 gauss-seidel spectral radius is 0.9821232 estimated iterations to convergence 62 setup time was (sec) 0.4900000 now iterating at: 11:34:36 rms-change max change #iterations 8.1486821E-02 14.69276 at 10iterations 5.6987377E-03 0.7741966 at 20iterations 6.9604471E-04 9.7347260E-02 at 30iterations 1.7671230E-04 2.2348404E-02 at 40iterations 5.4716631E-05 8.0409050E-03 at 50iterations finished qdiffx linear iterations at : 11:34:39 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 5.4716631E-05 8.0409050E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 11:34:39 3.615u 0.207s 0:04.22 90.2% 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 8 2011 at 11:34:39 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 = 4362 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: 1.606547 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): 59.82900 115.3300 ymin,ymax (A): 19.66500 81.52000 zmin,zma (A): -10.28500 56.19300 x,y,z range (A): 55.50100 61.85500 66.47800 scale (grids/A): 1.606547 object centre (A): 87.57950 50.59250 22.95400 number of atom coordinates read : 4362 total number of charged atoms : 4203 net assigned charge : -0.9999546 assigned positive charge : 654.5993 centred at (gu) : 88.36555 90.16865 90.37392 assigned negative charge : -655.6025 centred at (gu) : 88.91782 89.98401 89.95459 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 88329 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33896 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 27783 mr = 62952 m= 2864 mr = 19773 m= 76 mr = 1518 m= 0 mr = 6 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 5629 time to turn everything in is 0.4300000 number of dielectric boundary points 34803 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 428 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 32049 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) : 0.5355155 object centre at (A) : 87.57950 50.59250 22.95400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4429326E-02 1.7916873E-02 midg,1,midg; midg,igrid,midg -1.7731320E-02 2.5877036E-02 1,midg,midg; igrid,midg,midg 2.4383394E-02 -1.8349465E-02 gauss-seidel spectral radius is 0.9982548 estimated iterations to convergence 190 setup time was (sec) 0.6600000 now iterating at: 11:34:40 rms-change max change #iterations 4.006879 190.1069 at 10iterations 1.698482 57.56480 at 20iterations 0.7219825 24.80458 at 30iterations 0.3066446 9.447976 at 40iterations 0.1302772 3.893282 at 50iterations 5.5426028E-02 1.774429 at 60iterations 2.3700720E-02 0.7160492 at 70iterations 1.0106360E-02 0.3079758 at 80iterations 4.3686689E-03 0.1436974 at 90iterations 1.9152594E-03 6.4560890E-02 at 100iterations 8.6675375E-04 2.5901794E-02 at 110iterations 4.1776209E-04 1.4053345E-02 at 120iterations finished qdiffx linear iterations at : 11:34:48 total time elapsed so far: 8.190000 # loops : 120 mean,max change (kT/e) : 4.1776209E-04 1.4053345E-02 energy calculations done at 8.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.310000 DelPhi exited at 11:34:48 8.315u 0.245s 0:09.03 94.6% 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 Sat Oct 8 2011 at 11:34:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4362 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: 2.409820 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): 59.82900 115.3300 ymin,ymax (A): 19.66500 81.52000 zmin,zma (A): -10.28500 56.19300 x,y,z range (A): 55.50100 61.85500 66.47800 scale (grids/A): 2.409820 object centre (A): 87.57950 50.59250 22.95400 number of atom coordinates read : 4362 total number of charged atoms : 4203 net assigned charge : -0.9999546 assigned positive charge : 654.5993 centred at (gu) : 87.54791 90.25268 90.56051 assigned negative charge : -655.6025 centred at (gu) : 88.37669 89.97607 89.93178 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 205851 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33896 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 96826 mr = 153707 m= 27769 mr = 78348 m= 4453 mr = 21566 m= 271 mr = 2968 m= 2 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 19226 time to turn everything in is 1.070000 number of dielectric boundary points 78470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 33582 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) : 1.606547 object centre at (A) : 87.57950 50.59250 22.95400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1664196 0.3347039 midg,1,midg; midg,igrid,midg -0.4807009 0.5248647 1,midg,midg; igrid,midg,midg 0.4320007 -0.2581325 gauss-seidel spectral radius is 0.9991858 estimated iterations to convergence 277 setup time was (sec) 1.330000 now iterating at: 11:34:50 rms-change max change #iterations 10.44216 286.6838 at 10iterations 5.986475 132.7486 at 20iterations 3.404869 67.04045 at 30iterations 1.932632 36.26563 at 40iterations 1.092903 20.51817 at 50iterations 0.6161183 11.06251 at 60iterations 0.3476328 6.546488 at 70iterations 0.1955826 3.647094 at 80iterations 0.1097763 2.018939 at 90iterations 6.1654471E-02 1.112039 at 100iterations 3.4622241E-02 0.6442966 at 110iterations 1.9450976E-02 0.3539263 at 120iterations 1.0909151E-02 0.1974707 at 130iterations 6.1484585E-03 0.1066418 at 140iterations 3.4752265E-03 6.9295883E-02 at 150iterations 1.9786851E-03 3.9717674E-02 at 160iterations 1.1450229E-03 1.9737244E-02 at 170iterations 6.7675335E-04 1.4305115E-02 at 180iterations finished qdiffx linear iterations at : 11:35:02 total time elapsed so far: 13.43000 # loops : 180 mean,max change (kT/e) : 6.7675335E-04 1.4305115E-02 energy calculations done at 13.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.56000 DelPhi exited at 11:35:03 13.560u 0.248s 0:14.42 95.7% 0+0k 0+0io 0pf+0w