Mon Oct 10 09:44:24 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+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 09:44:24 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 !!! WARNING: HIT 230 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5688446 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): -18.48000 34.25600 ymin,ymax (A): -62.94300 -0.9120001 zmin,zma (A): -1.922000 60.66100 x,y,z range (A): 52.73600 62.03100 62.58300 scale (grids/A): 0.5688446 object centre (A): 7.887999 -31.92750 29.36950 number of atom coordinates read : 2809 total number of charged atoms : 2659 net assigned charge : 7.014012 assigned positive charge : 412.0769 centred at (gu) : 89.00613 88.61419 87.87140 assigned negative charge : -405.0634 centred at (gu) : 89.10480 88.44820 87.80458 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6253 nv = 96 ne = 84 npr = 53548 no. pairs analyzed = 53548 no. exposed pairs = 4285 no. arc points = 31345 no. surface atoms = 1421 nbur = 1388 mkacc time = 0.1300000 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 = 1.540000 m= 313 mr = 2700 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3065 ## 372 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7805 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0945341E-10 1.1991579E-09 midg,1,midg; midg,igrid,midg -1.7647394E-09 2.3658016E-09 1,midg,midg; igrid,midg,midg 3.0385703E-09 -2.2066039E-10 gauss-seidel spectral radius is 0.9840625 estimated iterations to convergence 65 setup time was (sec) 0.5500000 now iterating at: 09:44:25 rms-change max change #iterations 8.3537146E-02 14.30192 at 10iterations 6.0472679E-03 0.9413509 at 20iterations 4.9662008E-04 8.6277962E-02 at 30iterations 6.7248424E-05 9.6988678E-03 at 40iterations 1.5595764E-05 1.8917322E-03 at 50iterations finished qdiffx linear iterations at : 09:44:27 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.5595764E-05 1.8917322E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 09:44:28 3.391u 0.142s 0:03.81 92.6% 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 09:44:28 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 !!! WARNING: HIT 230 has a net charge of 0.5140 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: 1.706534 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): -18.48000 34.25600 ymin,ymax (A): -62.94300 -0.9120001 zmin,zma (A): -1.922000 60.66100 x,y,z range (A): 52.73600 62.03100 62.58300 scale (grids/A): 1.706534 object centre (A): 7.887999 -31.92750 29.36950 number of atom coordinates read : 2809 total number of charged atoms : 2659 net assigned charge : 7.014012 assigned positive charge : 412.0769 centred at (gu) : 87.01806 85.84225 83.61388 assigned negative charge : -405.0634 centred at (gu) : 87.31414 85.34408 83.41314 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 66549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31345 grid for indexing accessible points = 1.400000 m= 21360 mr = 40266 m= 2821 mr = 13573 m= 105 mr = 1244 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 35745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 315 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 20629 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) : 0.5688446 object centre at (A) : 7.887999 -31.92750 29.36950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2117446E-03 5.2346000E-03 midg,1,midg; midg,igrid,midg 1.1262025E-02 3.4815066E-02 1,midg,midg; igrid,midg,midg 9.6841780E-03 3.8480957E-03 gauss-seidel spectral radius is 0.9983504 estimated iterations to convergence 195 setup time was (sec) 0.8200000 now iterating at: 09:44:29 rms-change max change #iterations 3.490714 157.7287 at 10iterations 1.505802 54.14128 at 20iterations 0.6539284 27.17462 at 30iterations 0.2824417 9.951691 at 40iterations 0.1221916 4.505991 at 50iterations 5.3209420E-02 1.967560 at 60iterations 2.3097776E-02 0.8518448 at 70iterations 9.9950377E-03 0.3997059 at 80iterations 4.3514194E-03 0.1634383 at 90iterations 1.8895261E-03 6.8510056E-02 at 100iterations 8.2425226E-04 2.9144287E-02 at 110iterations 3.6434384E-04 1.2462616E-02 at 120iterations finished qdiffx linear iterations at : 09:44:35 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 3.6434384E-04 1.2462616E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 09:44:36 7.504u 0.169s 0:08.08 94.8% 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 09:44:36 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2809 !!! WARNING: HIT 230 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.559801 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): -18.48000 34.25600 ymin,ymax (A): -62.94300 -0.9120001 zmin,zma (A): -1.922000 60.66100 x,y,z range (A): 52.73600 62.03100 62.58300 scale (grids/A): 2.559801 object centre (A): 7.887999 -31.92750 29.36950 number of atom coordinates read : 2809 total number of charged atoms : 2659 net assigned charge : 7.014012 assigned positive charge : 412.0769 centred at (gu) : 85.52699 83.76319 80.42072 assigned negative charge : -405.0634 centred at (gu) : 85.97119 83.01606 80.11966 start vw surface at 0.1700000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 153849 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31345 grid for indexing accessible points = 1.400000 m= 69680 mr = 99742 m= 23057 mr = 51852 m= 4422 mr = 16426 m= 390 mr = 2592 m= 12 mr = 143 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 80655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 21263 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) : 1.706534 object centre at (A) : 7.887999 -31.92750 29.36950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2027422 8.4808148E-02 midg,1,midg; midg,igrid,midg 0.1512194 0.4195829 1,midg,midg; igrid,midg,midg 5.9347842E-02 4.1695695E-02 gauss-seidel spectral radius is 0.9992039 estimated iterations to convergence 280 setup time was (sec) 1.570000 now iterating at: 09:44:38 rms-change max change #iterations 9.160254 350.6032 at 10iterations 5.402608 150.5457 at 20iterations 3.134879 100.5721 at 30iterations 1.812847 50.94347 at 40iterations 1.038331 27.50897 at 50iterations 0.5931847 14.67200 at 60iterations 0.3381953 8.767208 at 70iterations 0.1922618 5.389568 at 80iterations 0.1091747 2.447032 at 90iterations 6.1734315E-02 1.567493 at 100iterations 3.4982856E-02 0.8858566 at 110iterations 1.9750891E-02 0.4308147 at 120iterations 1.1161170E-02 0.2937851 at 130iterations 6.2929117E-03 0.1419816 at 140iterations 3.5442682E-03 7.8306198E-02 at 150iterations 2.0001945E-03 4.4663429E-02 at 160iterations 1.1267969E-03 2.4856567E-02 at 170iterations 6.3451292E-04 1.4216304E-02 at 180iterations finished qdiffx linear iterations at : 09:44:48 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 6.3451292E-04 1.4216304E-02 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 09:44:49 12.069u 0.168s 0:12.52 97.6% 0+0k 0+0io 0pf+0w