Sun Oct 9 03:08:37 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 03:08:37 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.4437741 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): 15.71900 95.94000 ymin,ymax (A): -3.443000 54.88500 zmin,zma (A): 156.3790 222.6860 x,y,z range (A): 80.22100 58.32800 66.30699 scale (grids/A): 0.4437741 object centre (A): 55.82950 25.72100 189.5325 number of atom coordinates read : 4419 total number of charged atoms : 4187 net assigned charge : 19.00002 assigned positive charge : 643.1024 centred at (gu) : 94.85677 91.03914 88.50362 assigned negative charge : -624.1068 centred at (gu) : 94.89816 91.03132 88.55100 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 5242 nv = 96 ne = 84 npr = 89988 no. pairs analyzed = 89988 no. exposed pairs = 5568 no. arc points = 38905 no. surface atoms = 1897 nbur = 2522 mkacc time = 0.1900000 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 = 1.904000 m= 126 mr = 2511 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 2857 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3218 ## 622 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7063 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9335252E-11 3.0791214E-12 midg,1,midg; midg,igrid,midg 5.8603196E-12 1.2484081E-11 1,midg,midg; igrid,midg,midg 2.9403643E-12 2.1479670E-11 gauss-seidel spectral radius is 0.9740729 estimated iterations to convergence 52 setup time was (sec) 0.6300000 now iterating at: 03:08:38 rms-change max change #iterations 3.0993279E-02 6.371162 at 10iterations 2.6811706E-03 0.4643421 at 20iterations 5.9731968E-04 0.1107769 at 30iterations 1.4532334E-04 2.7748108E-02 at 40iterations 3.5511788E-05 6.8874359E-03 at 50iterations finished qdiffx linear iterations at : 03:08:40 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 3.5511788E-05 6.8874359E-03 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 03:08:41 3.250u 0.148s 0:03.75 90.4% 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 03:08:41 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.331322 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): 15.71900 95.94000 ymin,ymax (A): -3.443000 54.88500 zmin,zma (A): 156.3790 222.6860 x,y,z range (A): 80.22100 58.32800 66.30699 scale (grids/A): 1.331322 object centre (A): 55.82950 25.72100 189.5325 number of atom coordinates read : 4419 total number of charged atoms : 4187 net assigned charge : 19.00002 assigned positive charge : 643.1024 centred at (gu) : 104.5686 93.11531 85.50949 assigned negative charge : -624.1068 centred at (gu) : 104.6941 93.09348 85.65288 start vw surface at 0.1900000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 60893 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38905 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 14383 mr = 40247 m= 752 mr = 8755 m= 7 mr = 191 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 474 time to turn everything in is 0.4800000 number of dielectric boundary points 26842 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 623 ## 15 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 29563 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) : 0.4437741 object centre at (A) : 55.82950 25.72100 189.5325 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5135440E-03 2.0274487E-03 midg,1,midg; midg,igrid,midg 9.7484229E-04 1.4872601E-03 1,midg,midg; igrid,midg,midg 3.4381009E-03 2.1638600E-02 gauss-seidel spectral radius is 0.9973390 estimated iterations to convergence 155 setup time was (sec) 0.7400000 now iterating at: 03:08:42 rms-change max change #iterations 2.479603 116.0047 at 10iterations 0.8610495 35.10705 at 20iterations 0.3004519 11.64693 at 30iterations 0.1048541 3.876448 at 40iterations 3.6852982E-02 1.453588 at 50iterations 1.3057961E-02 0.5287762 at 60iterations 4.8412313E-03 0.2048588 at 70iterations 1.9535033E-03 8.0293179E-02 at 80iterations 9.0218137E-04 3.8841248E-02 at 90iterations 4.7728413E-04 2.0408630E-02 at 100iterations 2.7364274E-04 1.1573792E-02 at 110iterations 1.6310750E-04 6.9293976E-03 at 120iterations finished qdiffx linear iterations at : 03:08:47 total time elapsed so far: 6.640000 # loops : 120 mean,max change (kT/e) : 1.6310750E-04 6.9293976E-03 energy calculations done at 6.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.810000 DelPhi exited at 03:08:48 6.812u 0.150s 0:07.27 95.7% 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 03:08:48 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4419 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.996983 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): 15.71900 95.94000 ymin,ymax (A): -3.443000 54.88500 zmin,zma (A): 156.3790 222.6860 x,y,z range (A): 80.22100 58.32800 66.30699 scale (grids/A): 1.996983 object centre (A): 55.82950 25.72100 189.5325 number of atom coordinates read : 4419 total number of charged atoms : 4187 net assigned charge : 19.00002 assigned positive charge : 643.1024 centred at (gu) : 111.8528 94.67255 83.26376 assigned negative charge : -624.1068 centred at (gu) : 112.0411 94.64023 83.47920 start vw surface at 0.1800000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 142913 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38905 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 55411 mr = 100358 m= 10373 mr = 41373 m= 793 mr = 6718 m= 14 mr = 325 m= 0 mr = 0 time to grow re-entrant surface = 0.5600000 no. cavity mid-points inaccessible to solvent = 1663 time to turn everything in is 1.010000 number of dielectric boundary points 60730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 33138 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) : 1.331322 object centre at (A) : 55.82950 25.72100 189.5325 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3761699E-02 4.8604347E-02 midg,1,midg; midg,igrid,midg 2.0680144E-02 2.1862820E-02 1,midg,midg; igrid,midg,midg 5.2543566E-02 0.3616028 gauss-seidel spectral radius is 0.9988711 estimated iterations to convergence 236 setup time was (sec) 1.280000 now iterating at: 03:08:49 rms-change max change #iterations 7.413066 232.7516 at 10iterations 3.847706 102.7564 at 20iterations 1.990793 60.42650 at 30iterations 1.025094 27.70306 at 40iterations 0.5237530 15.28023 at 50iterations 0.2678472 7.208786 at 60iterations 0.1359677 3.171965 at 70iterations 6.9050908E-02 1.828925 at 80iterations 3.5099499E-02 0.8522949 at 90iterations 1.7787445E-02 0.4161530 at 100iterations 9.0524973E-03 0.2047528 at 110iterations 4.6211346E-03 0.1059799 at 120iterations 2.3602431E-03 5.3949594E-02 at 130iterations 1.2259746E-03 2.8774261E-02 at 140iterations 6.4883858E-04 1.9275665E-02 at 150iterations 3.5579660E-04 9.5481873E-03 at 160iterations 2.0537073E-04 5.1975250E-03 at 170iterations 1.2518054E-04 3.2157898E-03 at 180iterations finished qdiffx linear iterations at : 03:08:59 total time elapsed so far: 10.53000 # loops : 180 mean,max change (kT/e) : 1.2518054E-04 3.2157898E-03 energy calculations done at 10.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.73000 DelPhi exited at 03:08:59 10.729u 0.167s 0:11.16 97.4% 0+0k 0+0io 0pf+0w