Tue Oct 11 07:35:24 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 Tue Oct 11 2011 at 07:35:24 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 = 3639 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: 0.5416014 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): 10.91300 61.30300 ymin,ymax (A): -1.091000 64.64000 zmin,zma (A): -1.001000 50.16800 x,y,z range (A): 50.39000 65.73100 51.16900 scale (grids/A): 0.5416014 object centre (A): 36.10800 31.77450 24.58350 number of atom coordinates read : 3639 total number of charged atoms : 3494 net assigned charge : -1.499980 assigned positive charge : 548.3104 centred at (gu) : 90.29764 90.56329 90.45703 assigned negative charge : -549.8126 centred at (gu) : 90.43829 90.63556 90.38037 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6944 nv = 96 ne = 84 npr = 74645 no. pairs analyzed = 74645 no. exposed pairs = 4099 no. arc points = 28105 no. surface atoms = 1401 nbur = 2238 mkacc time = 0.2500000 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 = 1.568000 m= 275 mr = 4016 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.5000000 number of dielectric boundary points 3197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2873 ## 364 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 9094 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.4658356E-10 5.1183979E-10 midg,1,midg; midg,igrid,midg 3.6835265E-10 -6.7117195E-10 1,midg,midg; igrid,midg,midg 8.2428198E-10 -1.1555364E-09 gauss-seidel spectral radius is 0.9824705 estimated iterations to convergence 62 setup time was (sec) 0.8200000 now iterating at: 07:35:25 rms-change max change #iterations 7.9517491E-02 11.48647 at 10iterations 6.2220944E-03 0.9579010 at 20iterations 8.5704250E-04 0.1585960 at 30iterations 1.9717956E-04 3.8619995E-02 at 40iterations 4.8534421E-05 9.7694397E-03 at 50iterations finished qdiffx linear iterations at : 07:35:29 total time elapsed so far: 4.470000 # loops : 50 mean,max change (kT/e) : 4.8534421E-05 9.7694397E-03 energy calculations done at 4.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.700000 DelPhi exited at 07:35:30 4.708u 0.393s 0:05.71 89.1% 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 Tue Oct 11 2011 at 07:35:30 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 = 3639 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: 1.624804 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): 10.91300 61.30300 ymin,ymax (A): -1.091000 64.64000 zmin,zma (A): -1.001000 50.16800 x,y,z range (A): 50.39000 65.73100 51.16900 scale (grids/A): 1.624804 object centre (A): 36.10800 31.77450 24.58350 number of atom coordinates read : 3639 total number of charged atoms : 3494 net assigned charge : -1.499980 assigned positive charge : 548.3104 centred at (gu) : 90.89165 91.68884 91.36975 assigned negative charge : -549.8126 centred at (gu) : 91.31430 91.90634 91.14046 start vw surface at 0.1900000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 77224 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28105 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 26111 mr = 55556 m= 2666 mr = 19452 m= 64 mr = 1406 m= 0 mr = 9 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 2480 time to turn everything in is 0.7800000 number of dielectric boundary points 29642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 330 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 26729 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) : 0.5416014 object centre at (A) : 36.10800 31.77450 24.58350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2622514E-02 -1.5408801E-03 midg,1,midg; midg,igrid,midg 1.5447561E-02 -1.7552929E-02 1,midg,midg; igrid,midg,midg 9.1350097E-03 -1.0524254E-02 gauss-seidel spectral radius is 0.9982288 estimated iterations to convergence 189 setup time was (sec) 1.110000 now iterating at: 07:35:31 rms-change max change #iterations 3.735095 157.2596 at 10iterations 1.573683 60.72362 at 20iterations 0.6648248 23.23394 at 30iterations 0.2801623 9.596272 at 40iterations 0.1192056 4.043335 at 50iterations 5.0226435E-02 1.597618 at 60iterations 2.1275992E-02 0.7227249 at 70iterations 9.0883942E-03 0.2921205 at 80iterations 3.9145327E-03 0.1404915 at 90iterations 1.7022352E-03 6.8521500E-02 at 100iterations 7.5447769E-04 2.7320862E-02 at 110iterations 3.4407561E-04 1.2775421E-02 at 120iterations finished qdiffx linear iterations at : 07:35:40 total time elapsed so far: 10.28000 # loops : 120 mean,max change (kT/e) : 3.4407561E-04 1.2775421E-02 energy calculations done at 10.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.50000 DelPhi exited at 07:35:41 10.505u 0.450s 0:11.26 97.2% 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 07:35:41 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3639 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: 2.437206 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): 10.91300 61.30300 ymin,ymax (A): -1.091000 64.64000 zmin,zma (A): -1.001000 50.16800 x,y,z range (A): 50.39000 65.73100 51.16900 scale (grids/A): 2.437206 object centre (A): 36.10800 31.77450 24.58350 number of atom coordinates read : 3639 total number of charged atoms : 3494 net assigned charge : -1.499980 assigned positive charge : 548.3104 centred at (gu) : 91.33730 92.53316 92.05436 assigned negative charge : -549.8126 centred at (gu) : 91.97145 92.85942 91.71071 start vw surface at 0.1800000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 179420 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28105 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 89786 mr = 134780 m= 26752 mr = 74454 m= 4239 mr = 21357 m= 328 mr = 2973 m= 5 mr = 152 m= 0 mr = 2 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 8179 time to turn everything in is 1.940000 number of dielectric boundary points 66812 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 27902 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) : 1.624804 object centre at (A) : 36.10800 31.77450 24.58350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1542034 -3.7770842E-03 midg,1,midg; midg,igrid,midg 0.3719074 -0.4795291 1,midg,midg; igrid,midg,midg 0.1411394 -0.1473720 gauss-seidel spectral radius is 0.9991567 estimated iterations to convergence 272 setup time was (sec) 2.300000 now iterating at: 07:35:44 rms-change max change #iterations 9.452425 382.9568 at 10iterations 5.304694 110.8168 at 20iterations 2.969522 61.18667 at 30iterations 1.649781 37.24389 at 40iterations 0.9188441 17.82724 at 50iterations 0.5110129 9.628387 at 60iterations 0.2837959 5.526406 at 70iterations 0.1575368 2.954180 at 80iterations 8.7270148E-02 1.625180 at 90iterations 4.8420265E-02 0.9577150 at 100iterations 2.6875572E-02 0.5253563 at 110iterations 1.4906025E-02 0.2922401 at 120iterations 8.2949363E-03 0.1520844 at 130iterations 4.6365969E-03 8.5418701E-02 at 140iterations 2.5964514E-03 5.0315857E-02 at 150iterations 1.4711353E-03 2.7484894E-02 at 160iterations 8.4586366E-04 1.6983032E-02 at 170iterations 4.9585657E-04 9.9563599E-03 at 180iterations finished qdiffx linear iterations at : 07:35:59 total time elapsed so far: 17.99000 # loops : 180 mean,max change (kT/e) : 4.9585657E-04 9.9563599E-03 energy calculations done at 17.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.20000 DelPhi exited at 07:36:00 18.203u 0.487s 0:19.23 97.1% 0+0k 0+0io 0pf+0w