Tue Oct 11 06:02:46 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 Tue Oct 11 2011 at 06:02:46 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7060550 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): 25.70300 72.14200 ymin,ymax (A): -18.83100 31.59000 zmin,zma (A): 3.897000 46.35900 x,y,z range (A): 46.43900 50.42100 42.46200 scale (grids/A): 0.7060550 object centre (A): 48.92250 6.379500 25.12800 number of atom coordinates read : 2327 total number of charged atoms : 2000 net assigned charge : 6.039011 assigned positive charge : 327.7059 centred at (gu) : 89.23910 90.22054 90.36926 assigned negative charge : -321.6671 centred at (gu) : 89.36513 90.15915 90.45050 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7171 nv = 96 ne = 84 npr = 42805 no. pairs analyzed = 42805 no. exposed pairs = 2559 no. arc points = 17394 no. surface atoms = 879 nbur = 1448 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 484 mr = 4149 m= 1 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1641 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7999 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.2638032E-08 8.8478380E-09 midg,1,midg; midg,igrid,midg 1.7723769E-08 8.2504521E-08 1,midg,midg; igrid,midg,midg 1.2814968E-07 -1.1780783E-08 gauss-seidel spectral radius is 0.9895465 estimated iterations to convergence 80 setup time was (sec) 0.3600000 now iterating at: 06:02:47 rms-change max change #iterations 0.2025007 31.07970 at 10iterations 2.5579985E-02 3.192776 at 20iterations 3.3702615E-03 0.4972937 at 30iterations 5.6061579E-04 7.0862770E-02 at 40iterations 1.3867390E-04 1.7051697E-02 at 50iterations finished qdiffx linear iterations at : 06:02:49 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 1.3867390E-04 1.7051697E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 06:02:51 3.375u 0.173s 0:04.88 72.5% 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 06:02:51 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.118165 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): 25.70300 72.14200 ymin,ymax (A): -18.83100 31.59000 zmin,zma (A): 3.897000 46.35900 x,y,z range (A): 46.43900 50.42100 42.46200 scale (grids/A): 2.118165 object centre (A): 48.92250 6.379500 25.12800 number of atom coordinates read : 2327 total number of charged atoms : 2000 net assigned charge : 6.039011 assigned positive charge : 327.7059 centred at (gu) : 87.71713 90.66165 91.10770 assigned negative charge : -321.6671 centred at (gu) : 88.09523 90.47736 91.35154 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76193 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17394 grid for indexing accessible points = 1.400000 m= 31175 mr = 54490 m= 6084 mr = 23818 m= 577 mr = 4186 m= 17 mr = 296 m= 0 mr = 9 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 31247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15867 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) : 0.7060550 object centre at (A) : 48.92250 6.379500 25.12800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8738030E-02 2.6896099E-02 midg,1,midg; midg,igrid,midg 4.0264964E-02 3.0176539E-02 1,midg,midg; igrid,midg,midg 4.2981256E-02 -4.5327239E-02 gauss-seidel spectral radius is 0.9988295 estimated iterations to convergence 231 setup time was (sec) 0.6100000 now iterating at: 06:02:52 rms-change max change #iterations 4.706353 193.6716 at 10iterations 2.326621 77.23187 at 20iterations 1.153511 37.56292 at 30iterations 0.5732315 18.41181 at 40iterations 0.2838930 9.298990 at 50iterations 0.1411169 4.395134 at 60iterations 6.9942169E-02 1.971264 at 70iterations 3.4822993E-02 1.115620 at 80iterations 1.7456830E-02 0.5538464 at 90iterations 8.7481346E-03 0.2834167 at 100iterations 4.3964665E-03 0.1334400 at 110iterations 2.2655630E-03 6.6899776E-02 at 120iterations finished qdiffx linear iterations at : 06:02:59 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.2655630E-03 6.6899776E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 06:02:59 7.838u 0.210s 0:08.64 93.0% 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 06:03:00 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.177248 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): 25.70300 72.14200 ymin,ymax (A): -18.83100 31.59000 zmin,zma (A): 3.897000 46.35900 x,y,z range (A): 46.43900 50.42100 42.46200 scale (grids/A): 3.177248 object centre (A): 48.92250 6.379500 25.12800 number of atom coordinates read : 2327 total number of charged atoms : 2000 net assigned charge : 6.039011 assigned positive charge : 327.7059 centred at (gu) : 86.57577 90.99244 91.66158 assigned negative charge : -321.6671 centred at (gu) : 87.14294 90.71611 92.02726 start vw surface at 0.1000000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 175341 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17394 grid for indexing accessible points = 1.400000 m= 96841 mr = 130841 m= 39964 mr = 81185 m= 11608 mr = 33041 m= 2393 mr = 9143 m= 283 mr = 1756 m= 12 mr = 191 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 70285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 16000 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) : 2.118165 object centre at (A) : 48.92250 6.379500 25.12800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1101774 0.2282622 midg,1,midg; midg,igrid,midg 0.2975317 0.1330941 1,midg,midg; igrid,midg,midg 0.4275969 -0.5610409 gauss-seidel spectral radius is 0.9992961 estimated iterations to convergence 297 setup time was (sec) 1.440000 now iterating at: 06:03:01 rms-change max change #iterations 10.49876 430.9041 at 10iterations 6.209610 144.2471 at 20iterations 3.671314 94.90919 at 30iterations 2.161572 41.18897 at 40iterations 1.272024 24.60586 at 50iterations 0.7489636 17.49442 at 60iterations 0.4396251 10.00289 at 70iterations 0.2574818 4.582830 at 80iterations 0.1511433 2.803352 at 90iterations 8.8593617E-02 1.532097 at 100iterations 5.2039657E-02 1.009626 at 110iterations 3.0644784E-02 0.7030182 at 120iterations 1.8176632E-02 0.3271828 at 130iterations 1.0928571E-02 0.1987572 at 140iterations 6.6990992E-03 0.1184444 at 150iterations 4.2239237E-03 7.7522278E-02 at 160iterations 2.7896457E-03 6.1027527E-02 at 170iterations 1.9481269E-03 3.6914825E-02 at 180iterations finished qdiffx linear iterations at : 06:03:13 total time elapsed so far: 13.31000 # loops : 180 mean,max change (kT/e) : 1.9481269E-03 3.6914825E-02 energy calculations done at 13.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.44000 DelPhi exited at 06:03:14 13.443u 0.232s 0:14.37 95.1% 0+0k 0+0io 0pf+0w