Tue Oct 11 07:36:20 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 07:36:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2377 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: 0.6472610 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): -10.62400 39.93000 ymin,ymax (A): -14.35700 40.64400 zmin,zma (A): 7.324000 52.17400 x,y,z range (A): 50.55400 55.00100 44.85000 scale (grids/A): 0.6472610 object centre (A): 14.65300 13.14350 29.74900 number of atom coordinates read : 2377 total number of charged atoms : 2241 net assigned charge : 4.500007 assigned positive charge : 356.9563 centred at (gu) : 89.88040 88.33514 90.31785 assigned negative charge : -352.4567 centred at (gu) : 89.81180 88.32795 90.46778 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6593 nv = 96 ne = 84 npr = 48316 no. pairs analyzed = 48316 no. exposed pairs = 2938 no. arc points = 20143 no. surface atoms = 998 nbur = 1379 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 3628 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1981 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7857 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5328751E-08 -1.2274778E-08 midg,1,midg; midg,igrid,midg 1.0158420E-08 6.4618830E-09 1,midg,midg; igrid,midg,midg -7.6157208E-10 1.6472974E-08 gauss-seidel spectral radius is 0.9876085 estimated iterations to convergence 73 setup time was (sec) 0.3900000 now iterating at: 07:36:20 rms-change max change #iterations 0.1467474 23.44572 at 10iterations 1.5073296E-02 2.258879 at 20iterations 1.5192090E-03 0.2275801 at 30iterations 1.6024492E-04 2.3651123E-02 at 40iterations 1.9307428E-05 2.5072098E-03 at 50iterations finished qdiffx linear iterations at : 07:36:23 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.9307428E-05 2.5072098E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 07:36:24 3.432u 0.176s 0:04.23 85.1% 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 07:36:24 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 = 2377 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: 1.941783 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): -10.62400 39.93000 ymin,ymax (A): -14.35700 40.64400 zmin,zma (A): 7.324000 52.17400 x,y,z range (A): 50.55400 55.00100 44.85000 scale (grids/A): 1.941783 object centre (A): 14.65300 13.14350 29.74900 number of atom coordinates read : 2377 total number of charged atoms : 2241 net assigned charge : 4.500007 assigned positive charge : 356.9563 centred at (gu) : 89.64098 85.00493 90.95328 assigned negative charge : -352.4567 centred at (gu) : 89.43515 84.98380 91.40311 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 70054 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20143 grid for indexing accessible points = 1.400000 m= 27973 mr = 48420 m= 5015 mr = 21129 m= 286 mr = 3237 m= 1 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 30437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 17633 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) : 0.6472610 object centre at (A) : 14.65300 13.14350 29.74900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2075655E-02 -2.4982704E-02 midg,1,midg; midg,igrid,midg 1.1043224E-02 3.8505111E-02 1,midg,midg; igrid,midg,midg -3.3912128E-03 5.8392477E-03 gauss-seidel spectral radius is 0.9986608 estimated iterations to convergence 217 setup time was (sec) 0.5800000 now iterating at: 07:36:25 rms-change max change #iterations 4.167537 172.6603 at 10iterations 1.972616 83.44026 at 20iterations 0.9332783 31.51480 at 30iterations 0.4407648 13.62767 at 40iterations 0.2084321 7.478580 at 50iterations 9.8627798E-02 3.228376 at 60iterations 4.6526242E-02 1.506063 at 70iterations 2.1992866E-02 0.6801453 at 80iterations 1.0383109E-02 0.3444061 at 90iterations 4.9211844E-03 0.1449926 at 100iterations 2.3223450E-03 7.8163147E-02 at 110iterations 1.1067925E-03 3.8580418E-02 at 120iterations finished qdiffx linear iterations at : 07:36:32 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.1067925E-03 3.8580418E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 07:36:33 7.872u 0.206s 0:08.45 95.5% 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 07:36:33 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 = 2377 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: 2.912674 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): -10.62400 39.93000 ymin,ymax (A): -14.35700 40.64400 zmin,zma (A): 7.324000 52.17400 x,y,z range (A): 50.55400 55.00100 44.85000 scale (grids/A): 2.912674 object centre (A): 14.65300 13.14350 29.74900 number of atom coordinates read : 2377 total number of charged atoms : 2241 net assigned charge : 4.500007 assigned positive charge : 356.9563 centred at (gu) : 89.46124 82.50738 91.42982 assigned negative charge : -352.4567 centred at (gu) : 89.15269 82.47568 92.10461 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 161118 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20143 grid for indexing accessible points = 1.400000 m= 86636 mr = 116606 m= 35461 mr = 71631 m= 9356 mr = 29105 m= 1381 mr = 7155 m= 55 mr = 920 m= 0 mr = 25 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 68565 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 17923 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) : 1.941783 object centre at (A) : 14.65300 13.14350 29.74900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3836200 -0.3346018 midg,1,midg; midg,igrid,midg -0.1969667 0.4277435 1,midg,midg; igrid,midg,midg -4.2930685E-02 4.5298021E-03 gauss-seidel spectral radius is 0.9992594 estimated iterations to convergence 290 setup time was (sec) 1.160000 now iterating at: 07:36:34 rms-change max change #iterations 9.611506 348.2410 at 10iterations 5.606759 130.9672 at 20iterations 3.258888 68.06612 at 30iterations 1.886773 36.22128 at 40iterations 1.089559 24.69139 at 50iterations 0.6300080 11.59594 at 60iterations 0.3636282 7.626254 at 70iterations 0.2094431 4.273293 at 80iterations 0.1208140 2.366373 at 90iterations 6.9383703E-02 1.417721 at 100iterations 3.9983023E-02 0.7515427 at 110iterations 2.3011748E-02 0.4434900 at 120iterations 1.3233930E-02 0.2429237 at 130iterations 7.6149870E-03 0.1381450 at 140iterations 4.3808478E-03 8.0318451E-02 at 150iterations 2.5245761E-03 4.6451569E-02 at 160iterations 1.4581442E-03 2.7404785E-02 at 170iterations 8.4552541E-04 1.5802622E-02 at 180iterations finished qdiffx linear iterations at : 07:36:45 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 8.4552541E-04 1.5802622E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 07:36:46 12.425u 0.215s 0:13.00 97.1% 0+0k 0+0io 0pf+0w