Sat Oct 8 18:12:08 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 Sat Oct 8 2011 at 18:12:08 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3354 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5355235 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): -13.98000 41.40100 ymin,ymax (A): -38.56400 27.91300 zmin,zma (A): -17.44700 34.00300 x,y,z range (A): 55.38100 66.47701 51.45000 scale (grids/A): 0.5355235 object centre (A): 13.71050 -5.325501 8.277999 number of atom coordinates read : 3354 total number of charged atoms : 3209 net assigned charge : -1.499976 assigned positive charge : 504.6306 centred at (gu) : 90.78786 91.58389 90.82585 assigned negative charge : -506.1319 centred at (gu) : 90.77689 91.54436 90.77996 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6144 nv = 96 ne = 84 npr = 69225 no. pairs analyzed = 69225 no. exposed pairs = 3932 no. arc points = 27451 no. surface atoms = 1345 nbur = 2009 mkacc time = 0.1500000 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 = 1.596000 m= 219 mr = 3354 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3001 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2800 ## 398 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8059 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4421520E-10 2.0274266E-10 midg,1,midg; midg,igrid,midg -1.8024564E-10 1.9982457E-10 1,midg,midg; igrid,midg,midg -1.0106350E-10 -1.4019306E-11 gauss-seidel spectral radius is 0.9820496 estimated iterations to convergence 62 setup time was (sec) 0.5800000 now iterating at: 18:12:09 rms-change max change #iterations 7.0686340E-02 11.28675 at 10iterations 4.5876997E-03 0.7800808 at 20iterations 3.4902486E-04 6.6877365E-02 at 30iterations 5.0786941E-05 8.4156990E-03 at 40iterations 1.1199347E-05 1.9617081E-03 at 50iterations finished qdiffx linear iterations at : 18:12:11 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.1199347E-05 1.9617081E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 18:12:12 3.385u 0.199s 0:03.85 92.7% 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 8 2011 at 18:12:12 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3354 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.606571 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): -13.98000 41.40100 ymin,ymax (A): -38.56400 27.91300 zmin,zma (A): -17.44700 34.00300 x,y,z range (A): 55.38100 66.47701 51.45000 scale (grids/A): 1.606571 object centre (A): 13.71050 -5.325501 8.277999 number of atom coordinates read : 3354 total number of charged atoms : 3209 net assigned charge : -1.499976 assigned positive charge : 504.6306 centred at (gu) : 92.36313 94.75072 92.47686 assigned negative charge : -506.1319 centred at (gu) : 92.33033 94.63265 92.33916 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 68219 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27451 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20542 mr = 47819 m= 1927 mr = 14192 m= 55 mr = 910 m= 0 mr = 7 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 602 time to turn everything in is 0.5000000 number of dielectric boundary points 27815 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 370 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 24484 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) : 0.5355235 object centre at (A) : 13.71050 -5.325501 8.277999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6011669E-03 2.8589948E-03 midg,1,midg; midg,igrid,midg 5.4974137E-03 4.5254324E-03 1,midg,midg; igrid,midg,midg -3.2378114E-03 -1.2103139E-03 gauss-seidel spectral radius is 0.9981453 estimated iterations to convergence 184 setup time was (sec) 0.7800000 now iterating at: 18:12:13 rms-change max change #iterations 3.416372 137.8847 at 10iterations 1.410435 47.83960 at 20iterations 0.5837550 22.01580 at 30iterations 0.2416092 8.578236 at 40iterations 0.1000508 3.930985 at 50iterations 4.1533925E-02 1.710552 at 60iterations 1.7169321E-02 0.5951366 at 70iterations 7.1354639E-03 0.2512407 at 80iterations 2.9862409E-03 0.1040146 at 90iterations 1.2515362E-03 4.3067455E-02 at 100iterations 5.3657201E-04 1.8108368E-02 at 110iterations 2.3698655E-04 7.9116821E-03 at 120iterations finished qdiffx linear iterations at : 18:12:19 total time elapsed so far: 7.230000 # loops : 120 mean,max change (kT/e) : 2.3698655E-04 7.9116821E-03 energy calculations done at 7.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.420000 DelPhi exited at 18:12:20 7.418u 0.207s 0:07.90 96.3% 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 Sat Oct 8 2011 at 18:12:20 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3354 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.409856 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): -13.98000 41.40100 ymin,ymax (A): -38.56400 27.91300 zmin,zma (A): -17.44700 34.00300 x,y,z range (A): 55.38100 66.47701 51.45000 scale (grids/A): 2.409856 object centre (A): 13.71050 -5.325501 8.277999 number of atom coordinates read : 3354 total number of charged atoms : 3209 net assigned charge : -1.499976 assigned positive charge : 504.6306 centred at (gu) : 93.54434 97.12593 93.71507 assigned negative charge : -506.1319 centred at (gu) : 93.49536 96.94889 93.50865 start vw surface at 0.1600000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 158432 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27451 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 72694 mr = 116324 m= 19475 mr = 58162 m= 2971 mr = 14555 m= 192 mr = 1860 m= 9 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 2018 time to turn everything in is 1.180000 number of dielectric boundary points 62818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 25636 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) : 1.606571 object centre at (A) : 13.71050 -5.325501 8.277999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1176274 7.5844496E-02 midg,1,midg; midg,igrid,midg 5.6362830E-02 9.1164537E-02 1,midg,midg; igrid,midg,midg -6.1857726E-02 9.1244895E-03 gauss-seidel spectral radius is 0.9991265 estimated iterations to convergence 267 setup time was (sec) 1.480000 now iterating at: 18:12:21 rms-change max change #iterations 8.912100 262.3531 at 10iterations 4.994205 130.3372 at 20iterations 2.778200 56.13736 at 30iterations 1.538054 34.36848 at 40iterations 0.8498925 17.18076 at 50iterations 0.4676655 9.349194 at 60iterations 0.2579353 5.227825 at 70iterations 0.1418051 3.061262 at 80iterations 7.7823542E-02 1.731687 at 90iterations 4.2715546E-02 0.9230347 at 100iterations 2.3451321E-02 0.4788513 at 110iterations 1.2880166E-02 0.2665176 at 120iterations 7.0706643E-03 0.1570587 at 130iterations 3.8892312E-03 7.7892303E-02 at 140iterations 2.1326893E-03 4.1670799E-02 at 150iterations 1.1718218E-03 2.5959015E-02 at 160iterations 6.4704614E-04 1.4231682E-02 at 170iterations 3.5738357E-04 7.7400208E-03 at 180iterations finished qdiffx linear iterations at : 18:12:31 total time elapsed so far: 11.60000 # loops : 180 mean,max change (kT/e) : 3.5738357E-04 7.7400208E-03 energy calculations done at 11.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.77000 DelPhi exited at 18:12:32 11.768u 0.233s 0:12.26 97.7% 0+0k 0+0io 0pf+0w