Mon Oct 10 18:35:52 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 Mon Oct 10 2011 at 18:35:52 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 = 2363 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7029461 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): -41.96100 4.183000 ymin,ymax (A): 57.29500 107.9390 zmin,zma (A): -20.47300 29.52700 x,y,z range (A): 46.14400 50.64400 50.00000 scale (grids/A): 0.7029461 object centre (A): -18.88900 82.61700 4.527000 number of atom coordinates read : 2363 total number of charged atoms : 2226 net assigned charge : 1.000005 assigned positive charge : 352.2820 centred at (gu) : 89.24028 87.59796 88.62775 assigned negative charge : -351.2826 centred at (gu) : 89.17119 87.72883 88.59200 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7980 nv = 96 ne = 84 npr = 48145 no. pairs analyzed = 48145 no. exposed pairs = 2975 no. arc points = 20880 no. surface atoms = 1004 nbur = 1359 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 571 mr = 4473 m= 3 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.2000000 number of dielectric boundary points 3971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1830 ## 146 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8850 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5389597E-08 1.8486872E-08 midg,1,midg; midg,igrid,midg 1.1525073E-07 -3.7035381E-08 1,midg,midg; igrid,midg,midg -3.3121555E-08 3.4971947E-08 gauss-seidel spectral radius is 0.9894871 estimated iterations to convergence 79 setup time was (sec) 0.3700000 now iterating at: 18:35:52 rms-change max change #iterations 0.2095538 34.72784 at 10iterations 2.5569664E-02 3.322170 at 20iterations 3.0759922E-03 0.3782268 at 30iterations 3.9129754E-04 4.7178268E-02 at 40iterations 5.4423079E-05 7.3280334E-03 at 50iterations finished qdiffx linear iterations at : 18:35:55 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 5.4423079E-05 7.3280334E-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) 3.390000 DelPhi exited at 18:35:56 3.395u 0.177s 0:03.94 90.3% 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 Mon Oct 10 2011 at 18:35:56 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 = 2363 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: 2.108838 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): -41.96100 4.183000 ymin,ymax (A): 57.29500 107.9390 zmin,zma (A): -20.47300 29.52700 x,y,z range (A): 46.14400 50.64400 50.00000 scale (grids/A): 2.108838 object centre (A): -18.88900 82.61700 4.527000 number of atom coordinates read : 2363 total number of charged atoms : 2226 net assigned charge : 1.000005 assigned positive charge : 352.2820 centred at (gu) : 87.72015 82.79335 85.88287 assigned negative charge : -351.2826 centred at (gu) : 87.51342 83.18643 85.77576 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 83725 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20880 grid for indexing accessible points = 1.400000 m= 34345 mr = 58087 m= 7593 mr = 26268 m= 678 mr = 5294 m= 19 mr = 309 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1096 time to turn everything in is 0.4400000 number of dielectric boundary points 36402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 17708 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) : 0.7029461 object centre at (A) : -18.88900 82.61700 4.527000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.7588105E-03 1.6158540E-02 midg,1,midg; midg,igrid,midg 4.1753866E-02 -2.6169401E-02 1,midg,midg; igrid,midg,midg -1.9202727E-03 1.8788466E-02 gauss-seidel spectral radius is 0.9988499 estimated iterations to convergence 233 setup time was (sec) 0.6500000 now iterating at: 18:35:57 rms-change max change #iterations 4.887570 214.6925 at 10iterations 2.419798 78.96796 at 20iterations 1.207524 40.51813 at 30iterations 0.6031983 17.63914 at 40iterations 0.3010964 8.764580 at 50iterations 0.1499083 4.484972 at 60iterations 7.4634574E-02 2.433481 at 70iterations 3.7261985E-02 1.027126 at 80iterations 1.8656911E-02 0.5361567 at 90iterations 9.2856232E-03 0.2462616 at 100iterations 4.6429317E-03 0.1458387 at 110iterations 2.3204281E-03 6.5051317E-02 at 120iterations finished qdiffx linear iterations at : 18:36:04 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.3204281E-03 6.5051317E-02 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.970000 DelPhi exited at 18:36:04 7.975u 0.210s 0:08.60 95.1% 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 Mon Oct 10 2011 at 18:36:04 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 = 2363 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: 3.163257 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): -41.96100 4.183000 ymin,ymax (A): 57.29500 107.9390 zmin,zma (A): -20.47300 29.52700 x,y,z range (A): 46.14400 50.64400 50.00000 scale (grids/A): 3.163257 object centre (A): -18.88900 82.61700 4.527000 number of atom coordinates read : 2363 total number of charged atoms : 2226 net assigned charge : 1.000005 assigned positive charge : 352.2820 centred at (gu) : 86.58018 79.18987 83.82417 assigned negative charge : -351.2826 centred at (gu) : 86.27007 79.77968 83.66354 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 192664 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20880 grid for indexing accessible points = 1.400000 m= 104394 mr = 139683 m= 46243 mr = 86748 m= 14658 mr = 38789 m= 2888 mr = 11630 m= 247 mr = 2045 m= 5 mr = 133 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 3840 time to turn everything in is 1.320000 number of dielectric boundary points 82071 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 17808 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) : 2.108838 object centre at (A) : -18.88900 82.61700 4.527000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2613303E-02 0.8399595 midg,1,midg; midg,igrid,midg 0.3014877 -7.0624180E-02 1,midg,midg; igrid,midg,midg 9.4886171E-03 0.1006482 gauss-seidel spectral radius is 0.9993130 estimated iterations to convergence 301 setup time was (sec) 1.560000 now iterating at: 18:36:06 rms-change max change #iterations 11.02750 426.0952 at 10iterations 6.570086 145.6347 at 20iterations 3.900027 67.66087 at 30iterations 2.305659 46.77495 at 40iterations 1.366261 23.21477 at 50iterations 0.8061618 13.88510 at 60iterations 0.4744435 8.805062 at 70iterations 0.2789356 4.612428 at 80iterations 0.1640585 2.684723 at 90iterations 9.6429117E-02 1.531482 at 100iterations 5.6697812E-02 0.9339871 at 110iterations 3.3300586E-02 0.5380898 at 120iterations 1.9567205E-02 0.3094130 at 130iterations 1.1528210E-02 0.1763916 at 140iterations 6.8079969E-03 0.1152649 at 150iterations 4.0270989E-03 7.1678162E-02 at 160iterations 2.4058414E-03 4.0397644E-02 at 170iterations 1.4545786E-03 2.5394440E-02 at 180iterations finished qdiffx linear iterations at : 18:36:18 total time elapsed so far: 13.16000 # loops : 180 mean,max change (kT/e) : 1.4545786E-03 2.5394440E-02 energy calculations done at 13.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.29000 DelPhi exited at 18:36:18 13.294u 0.210s 0:13.82 97.6% 0+0k 0+0io 0pf+0w