Sat Oct 15 11:52:57 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 Sat Oct 15 2011 at 11:52:57 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2478 !!! WARNING: HIT 84 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6356575 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): -29.69700 26.30800 ymin,ymax (A): 9.054000 50.89200 zmin,zma (A): -12.10300 42.94400 x,y,z range (A): 56.00500 41.83800 55.04700 scale (grids/A): 0.6356575 object centre (A): -1.694500 29.97300 15.42050 number of atom coordinates read : 2478 total number of charged atoms : 2341 net assigned charge : 10.51403 assigned positive charge : 366.7761 centred at (gu) : 90.60720 90.57086 90.94520 assigned negative charge : -356.2629 centred at (gu) : 90.48128 90.48782 90.96675 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6995 nv = 96 ne = 84 npr = 48776 no. pairs analyzed = 48776 no. exposed pairs = 3374 no. arc points = 24182 no. surface atoms = 1121 nbur = 1357 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 415 mr = 3571 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2800000 number of dielectric boundary points 3796 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2342 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8194 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2670743E-08 1.3777291E-08 midg,1,midg; midg,igrid,midg 4.8682893E-09 2.3937192E-08 1,midg,midg; igrid,midg,midg 1.1876360E-09 2.8672494E-08 gauss-seidel spectral radius is 0.9871814 estimated iterations to convergence 72 setup time was (sec) 0.5700000 now iterating at: 11:52:58 rms-change max change #iterations 0.1386832 23.67896 at 10iterations 1.3245830E-02 2.422422 at 20iterations 1.3566324E-03 0.1938486 at 30iterations 1.7224056E-04 2.8259277E-02 at 40iterations 3.5059296E-05 6.2408447E-03 at 50iterations finished qdiffx linear iterations at : 11:53:02 total time elapsed so far: 4.100000 # loops : 50 mean,max change (kT/e) : 3.5059296E-05 6.2408447E-03 energy calculations done at 4.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.280000 DelPhi exited at 11:53:02 4.288u 0.243s 0:05.01 90.2% 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 Sat Oct 15 2011 at 11:53:02 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2478 !!! WARNING: HIT 84 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.906973 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): -29.69700 26.30800 ymin,ymax (A): 9.054000 50.89200 zmin,zma (A): -12.10300 42.94400 x,y,z range (A): 56.00500 41.83800 55.04700 scale (grids/A): 1.906973 object centre (A): -1.694500 29.97300 15.42050 number of atom coordinates read : 2478 total number of charged atoms : 2341 net assigned charge : 10.51403 assigned positive charge : 366.7761 centred at (gu) : 91.82125 91.71227 92.83502 assigned negative charge : -356.2629 centred at (gu) : 91.44390 91.46340 92.90032 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24182 grid for indexing accessible points = 1.400000 m= 26887 mr = 49272 m= 4576 mr = 19015 m= 301 mr = 2636 m= 5 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 312 time to turn everything in is 0.5800000 number of dielectric boundary points 35052 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 18380 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) : 0.6356575 object centre at (A) : -1.694500 29.97300 15.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4313518E-02 3.6668833E-02 midg,1,midg; midg,igrid,midg 1.3881127E-03 2.7672488E-02 1,midg,midg; igrid,midg,midg -6.7865113E-03 6.0799647E-02 gauss-seidel spectral radius is 0.9986466 estimated iterations to convergence 215 setup time was (sec) 0.9000000 now iterating at: 11:53:04 rms-change max change #iterations 4.107142 206.9901 at 10iterations 1.919917 68.20736 at 20iterations 0.9003814 31.43486 at 30iterations 0.4218167 13.94899 at 40iterations 0.1972215 7.326248 at 50iterations 9.2731491E-02 3.136798 at 60iterations 4.3615300E-02 1.355473 at 70iterations 2.0448910E-02 0.6369724 at 80iterations 9.6229082E-03 0.2929211 at 90iterations 4.5019556E-03 0.1503057 at 100iterations 2.1303196E-03 6.9486618E-02 at 110iterations 1.0096066E-03 3.3239365E-02 at 120iterations finished qdiffx linear iterations at : 11:53:12 total time elapsed so far: 9.690000 # loops : 120 mean,max change (kT/e) : 1.0096066E-03 3.3239365E-02 energy calculations done at 9.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.880000 DelPhi exited at 11:53:13 9.883u 0.296s 0:10.59 96.0% 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 Sat Oct 15 2011 at 11:53:13 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2478 !!! WARNING: HIT 84 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.860459 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): -29.69700 26.30800 ymin,ymax (A): 9.054000 50.89200 zmin,zma (A): -12.10300 42.94400 x,y,z range (A): 56.00500 41.83800 55.04700 scale (grids/A): 2.860459 object centre (A): -1.694500 29.97300 15.42050 number of atom coordinates read : 2478 total number of charged atoms : 2341 net assigned charge : 10.51403 assigned positive charge : 366.7761 centred at (gu) : 92.73173 92.56829 94.25246 assigned negative charge : -356.2629 centred at (gu) : 92.16589 92.19519 94.35048 start vw surface at 0.1400000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 171573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24182 grid for indexing accessible points = 1.400000 m= 85835 mr = 120097 m= 31981 mr = 68195 m= 8166 mr = 24859 m= 1298 mr = 5873 m= 97 mr = 795 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 1043 time to turn everything in is 1.470000 number of dielectric boundary points 79093 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 18726 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) : 1.906973 object centre at (A) : -1.694500 29.97300 15.42050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7460350 0.4099480 midg,1,midg; midg,igrid,midg 7.5009968E-03 0.2506665 1,midg,midg; igrid,midg,midg -4.7985371E-02 0.5567244 gauss-seidel spectral radius is 0.9992778 estimated iterations to convergence 294 setup time was (sec) 1.820000 now iterating at: 11:53:15 rms-change max change #iterations 9.856608 349.1308 at 10iterations 5.838999 154.5750 at 20iterations 3.435054 82.16648 at 30iterations 2.018446 49.09782 at 40iterations 1.180601 26.85295 at 50iterations 0.6903897 14.80067 at 60iterations 0.4024133 7.690435 at 70iterations 0.2339979 5.412440 at 80iterations 0.1361972 2.981415 at 90iterations 7.8846440E-02 1.494542 at 100iterations 4.5838915E-02 0.8687234 at 110iterations 2.6587456E-02 0.5021849 at 120iterations 1.5405963E-02 0.2994232 at 130iterations 8.9500919E-03 0.1895332 at 140iterations 5.1685143E-03 9.8279953E-02 at 150iterations 3.0006587E-03 5.8815055E-02 at 160iterations 1.7402569E-03 3.5228729E-02 at 170iterations 1.0120055E-03 1.9420624E-02 at 180iterations finished qdiffx linear iterations at : 11:53:29 total time elapsed so far: 15.85000 # loops : 180 mean,max change (kT/e) : 1.0120055E-03 1.9420624E-02 energy calculations done at 15.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.03000 DelPhi exited at 11:53:30 16.034u 0.314s 0:16.64 98.1% 0+0k 0+0io 0pf+0w