Tue Oct 11 06:03:57 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 Tue Oct 11 2011 at 06:03:57 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7314718 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): 25.64100 72.02500 ymin,ymax (A): -18.64100 30.02800 zmin,zma (A): 3.879000 46.39100 x,y,z range (A): 46.38400 48.66900 42.51200 scale (grids/A): 0.7314718 object centre (A): 48.83300 5.693501 25.13500 number of atom coordinates read : 2281 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 318.3760 centred at (gu) : 89.11050 90.50444 90.29102 assigned negative charge : -312.4312 centred at (gu) : 89.24797 90.43642 90.37421 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7665 nv = 96 ne = 84 npr = 41821 no. pairs analyzed = 41821 no. exposed pairs = 2559 no. arc points = 17416 no. surface atoms = 876 nbur = 1405 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 553 mr = 4483 m= 5 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3616 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1545 ## 134 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8194 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4620099E-07 1.6653791E-08 midg,1,midg; midg,igrid,midg 2.6633266E-08 1.5601107E-07 1,midg,midg; igrid,midg,midg 2.3504475E-07 -2.4529761E-08 gauss-seidel spectral radius is 0.9902529 estimated iterations to convergence 82 setup time was (sec) 0.5400000 now iterating at: 06:03:58 rms-change max change #iterations 0.2285844 29.93958 at 10iterations 3.0752575E-02 4.484253 at 20iterations 4.5591644E-03 0.5721626 at 30iterations 8.6438598E-04 9.1453552E-02 at 40iterations 2.5008078E-04 2.8041840E-02 at 50iterations finished qdiffx linear iterations at : 06:04:00 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 2.5008078E-04 2.8041840E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 06:04:01 3.315u 0.196s 0:04.20 83.3% 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 Tue Oct 11 2011 at 06:04:01 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.194415 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): 25.64100 72.02500 ymin,ymax (A): -18.64100 30.02800 zmin,zma (A): 3.879000 46.39100 x,y,z range (A): 46.38400 48.66900 42.51200 scale (grids/A): 2.194415 object centre (A): 48.83300 5.693501 25.13500 number of atom coordinates read : 2281 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 318.3760 centred at (gu) : 87.33166 91.51349 90.87317 assigned negative charge : -312.4312 centred at (gu) : 87.74411 91.30936 91.12270 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80838 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17416 grid for indexing accessible points = 1.400000 m= 34217 mr = 58004 m= 7367 mr = 26404 m= 765 mr = 5137 m= 24 mr = 467 m= 0 mr = 3 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 33196 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 56 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15536 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) : 0.7314718 object centre at (A) : 48.83300 5.693501 25.13500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3780037E-02 3.0018128E-02 midg,1,midg; midg,igrid,midg 4.3837305E-02 3.4165766E-02 1,midg,midg; igrid,midg,midg 4.9445372E-02 -5.9552573E-02 gauss-seidel spectral radius is 0.9988975 estimated iterations to convergence 238 setup time was (sec) 0.9100000 now iterating at: 06:04:02 rms-change max change #iterations 4.899570 182.8848 at 10iterations 2.472652 82.69341 at 20iterations 1.252998 35.83815 at 30iterations 0.6343148 19.85312 at 40iterations 0.3211185 9.906807 at 50iterations 0.1635029 4.578217 at 60iterations 8.2867980E-02 2.331100 at 70iterations 4.2156406E-02 1.186321 at 80iterations 2.1551350E-02 0.7017593 at 90iterations 1.1123691E-02 0.3488903 at 100iterations 5.7591656E-03 0.1707096 at 110iterations 3.0757259E-03 8.4350586E-02 at 120iterations finished qdiffx linear iterations at : 06:04:09 total time elapsed so far: 7.430000 # loops : 120 mean,max change (kT/e) : 3.0757259E-03 8.4350586E-02 energy calculations done at 7.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.600000 DelPhi exited at 06:04:09 7.605u 0.221s 0:08.15 95.9% 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 Tue Oct 11 2011 at 06:04:09 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.291623 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): 25.64100 72.02500 ymin,ymax (A): -18.64100 30.02800 zmin,zma (A): 3.879000 46.39100 x,y,z range (A): 46.38400 48.66900 42.51200 scale (grids/A): 3.291623 object centre (A): 48.83300 5.693501 25.13500 number of atom coordinates read : 2281 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 318.3760 centred at (gu) : 85.99738 92.27024 91.30972 assigned negative charge : -312.4312 centred at (gu) : 86.61618 91.96403 91.68404 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 186183 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17416 grid for indexing accessible points = 1.400000 m= 104340 mr = 139132 m= 45085 mr = 87725 m= 13933 mr = 37498 m= 3153 mr = 11160 m= 446 mr = 2407 m= 30 mr = 339 m= 0 mr = 13 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.890000 number of dielectric boundary points 74896 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.010000 number of grid points assigned charge 15640 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) : 2.194415 object centre at (A) : 48.83300 5.693501 25.13500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1088031 0.2626749 midg,1,midg; midg,igrid,midg 0.3095675 0.1908504 1,midg,midg; igrid,midg,midg 0.4643804 -0.6945701 gauss-seidel spectral radius is 0.9993131 estimated iterations to convergence 301 setup time was (sec) 2.170000 now iterating at: 06:04:12 rms-change max change #iterations 10.69739 307.2881 at 10iterations 6.371844 124.4986 at 20iterations 3.792254 70.36134 at 30iterations 2.259690 41.49868 at 40iterations 1.339387 24.21220 at 50iterations 0.7918960 14.04621 at 60iterations 0.4683939 8.204308 at 70iterations 0.2764439 5.104634 at 80iterations 0.1636853 2.705856 at 90iterations 9.6571028E-02 2.075809 at 100iterations 5.7089407E-02 1.048185 at 110iterations 3.4018617E-02 0.5993042 at 120iterations 2.0348614E-02 0.3900871 at 130iterations 1.2414718E-02 0.2289505 at 140iterations 7.7746389E-03 0.1396313 at 150iterations 5.0731418E-03 9.5542908E-02 at 160iterations 3.5042209E-03 6.1523438E-02 at 170iterations 2.5796129E-03 4.4670105E-02 at 180iterations finished qdiffx linear iterations at : 06:04:21 total time elapsed so far: 11.78000 # loops : 180 mean,max change (kT/e) : 2.5796129E-03 4.4670105E-02 energy calculations done at 11.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 06:04:22 11.971u 0.203s 0:12.97 93.8% 0+0k 0+0io 0pf+0w