Mon Oct 10 17:05:09 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 Mon Oct 10 2011 at 17:05:09 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3184 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5928294 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): -25.35700 32.65700 ymin,ymax (A): -9.234000 43.28800 zmin,zma (A): 7.067000 67.11800 x,y,z range (A): 58.01400 52.52200 60.05100 scale (grids/A): 0.5928294 object centre (A): 3.649999 17.02700 37.09250 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -5.257957 assigned positive charge : 482.0836 centred at (gu) : 90.21507 88.68050 91.26771 assigned negative charge : -487.3429 centred at (gu) : 90.28961 88.52554 91.37437 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7368 nv = 96 ne = 84 npr = 63807 no. pairs analyzed = 63807 no. exposed pairs = 4225 no. arc points = 29515 no. surface atoms = 1424 nbur = 1760 mkacc time = 0.1400000 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 = 1.484000 m= 334 mr = 3799 m= 0 mr = 20 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3200000 number of dielectric boundary points 3883 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2995 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9341 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6344243E-09 -7.4511686E-09 midg,1,midg; midg,igrid,midg -1.0019726E-08 2.8718774E-09 1,midg,midg; igrid,midg,midg 1.0167461E-09 -4.5783937E-09 gauss-seidel spectral radius is 0.9853302 estimated iterations to convergence 68 setup time was (sec) 0.5400000 now iterating at: 17:05:10 rms-change max change #iterations 0.1141718 16.93649 at 10iterations 9.5458180E-03 1.418129 at 20iterations 7.9480739E-04 0.1424389 at 30iterations 7.1791459E-05 1.1834145E-02 at 40iterations 1.0164840E-05 1.9721985E-03 at 50iterations finished qdiffx linear iterations at : 17:05:13 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 1.0164840E-05 1.9721985E-03 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.230000 DelPhi exited at 17:05:13 3.232u 0.185s 0:03.87 88.1% 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 17:05:13 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3184 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.778488 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): -25.35700 32.65700 ymin,ymax (A): -9.234000 43.28800 zmin,zma (A): 7.067000 67.11800 x,y,z range (A): 58.01400 52.52200 60.05100 scale (grids/A): 1.778488 object centre (A): 3.649999 17.02700 37.09250 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -5.257957 assigned positive charge : 482.0836 centred at (gu) : 90.64450 86.04076 93.80206 assigned negative charge : -487.3429 centred at (gu) : 90.86855 85.57626 94.12273 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 81062 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29515 grid for indexing accessible points = 1.400000 m= 25998 mr = 54685 m= 3097 mr = 17772 m= 123 mr = 1589 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1405 time to turn everything in is 0.5600000 number of dielectric boundary points 36208 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 255 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 23706 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) : 0.5928294 object centre at (A) : 3.649999 17.02700 37.09250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8722951E-02 4.9513574E-03 midg,1,midg; midg,igrid,midg -4.8311662E-02 6.7073242E-03 1,midg,midg; igrid,midg,midg 1.7556116E-02 -3.9493881E-02 gauss-seidel spectral radius is 0.9984998 estimated iterations to convergence 205 setup time was (sec) 0.8600000 now iterating at: 17:05:14 rms-change max change #iterations 4.226758 188.1898 at 10iterations 1.889622 65.71124 at 20iterations 0.8511537 28.91942 at 30iterations 0.3827280 12.59048 at 40iterations 0.1731324 5.837611 at 50iterations 7.7968568E-02 2.599643 at 60iterations 3.5188355E-02 1.129469 at 70iterations 1.5910970E-02 0.5099976 at 80iterations 7.1606054E-03 0.2179871 at 90iterations 3.2392200E-03 0.1066637 at 100iterations 1.4602420E-03 4.6629369E-02 at 110iterations 6.6083536E-04 2.2075653E-02 at 120iterations finished qdiffx linear iterations at : 17:05:21 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 6.6083536E-04 2.2075653E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 17:05:21 7.525u 0.193s 0:08.05 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 Mon Oct 10 2011 at 17:05:22 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3184 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: GLN 355 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.667732 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): -25.35700 32.65700 ymin,ymax (A): -9.234000 43.28800 zmin,zma (A): 7.067000 67.11800 x,y,z range (A): 58.01400 52.52200 60.05100 scale (grids/A): 2.667732 object centre (A): 3.649999 17.02700 37.09250 number of atom coordinates read : 3184 total number of charged atoms : 3041 net assigned charge : -5.257957 assigned positive charge : 482.0836 centred at (gu) : 90.96652 84.06082 95.70312 assigned negative charge : -487.3429 centred at (gu) : 91.30279 83.36415 96.18400 start vw surface at 0.1700000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 188005 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29515 grid for indexing accessible points = 1.400000 m= 87500 mr = 133668 m= 27018 mr = 68812 m= 4986 mr = 20233 m= 533 mr = 3327 m= 15 mr = 290 m= 0 mr = 3 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 4596 time to turn everything in is 1.370000 number of dielectric boundary points 81724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 24322 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) : 1.778488 object centre at (A) : 3.649999 17.02700 37.09250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4699084 0.1977628 midg,1,midg; midg,igrid,midg -0.6123160 0.1001180 1,midg,midg; igrid,midg,midg 0.3632590 -0.4513807 gauss-seidel spectral radius is 0.9992458 estimated iterations to convergence 287 setup time was (sec) 1.670000 now iterating at: 17:05:24 rms-change max change #iterations 10.50970 339.5385 at 10iterations 6.177873 142.9128 at 20iterations 3.600246 79.96751 at 30iterations 2.090345 44.56967 at 40iterations 1.209735 25.95356 at 50iterations 0.6975555 13.21215 at 60iterations 0.4014802 7.809578 at 70iterations 0.2304207 4.247407 at 80iterations 0.1321369 2.652121 at 90iterations 7.5849548E-02 1.410167 at 100iterations 4.3415595E-02 0.8336926 at 110iterations 2.4885934E-02 0.4576645 at 120iterations 1.4238589E-02 0.2916718 at 130iterations 8.1412140E-03 0.1416550 at 140iterations 4.6697105E-03 8.7745667E-02 at 150iterations 2.6663404E-03 4.6129227E-02 at 160iterations 1.5237692E-03 2.6357651E-02 at 170iterations 8.7302737E-04 1.4916420E-02 at 180iterations finished qdiffx linear iterations at : 17:05:34 total time elapsed so far: 11.66000 # loops : 180 mean,max change (kT/e) : 8.7302737E-04 1.4916420E-02 energy calculations done at 11.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.84000 DelPhi exited at 17:05:35 11.841u 0.202s 0:12.57 95.7% 0+0k 0+0io 0pf+0w