Sat Oct 8 23:08:48 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 Sat Oct 8 2011 at 23:08:48 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 = 2423 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: 0.6471080 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): -13.83800 41.17600 ymin,ymax (A): 12.44900 65.45600 zmin,zma (A): 3.136000 45.66000 x,y,z range (A): 55.01400 53.00700 42.52400 scale (grids/A): 0.6471080 object centre (A): 13.66900 38.95250 24.39800 number of atom coordinates read : 2423 total number of charged atoms : 2287 net assigned charge : 12.00002 assigned positive charge : 354.8472 centred at (gu) : 89.93017 88.98003 89.12162 assigned negative charge : -342.8480 centred at (gu) : 89.97942 88.97269 89.20541 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6973 nv = 96 ne = 84 npr = 48564 no. pairs analyzed = 48564 no. exposed pairs = 3117 no. arc points = 22461 no. surface atoms = 1044 nbur = 1379 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 417 mr = 3742 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.2800000 number of dielectric boundary points 3585 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2113 ## 169 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8100 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7979788E-08 9.0553183E-09 midg,1,midg; midg,igrid,midg 2.5068779E-08 1.8010747E-08 1,midg,midg; igrid,midg,midg 2.7757448E-08 1.4874254E-08 gauss-seidel spectral radius is 0.9876173 estimated iterations to convergence 73 setup time was (sec) 0.5700000 now iterating at: 23:08:49 rms-change max change #iterations 0.1437335 26.53722 at 10iterations 1.4457263E-02 1.903874 at 20iterations 1.5945196E-03 0.2623558 at 30iterations 2.6755410E-04 4.7280312E-02 at 40iterations 7.6039032E-05 1.5909195E-02 at 50iterations finished qdiffx linear iterations at : 23:08:53 total time elapsed so far: 4.280000 # loops : 50 mean,max change (kT/e) : 7.6039032E-05 1.5909195E-02 energy calculations done at 4.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 23:08:53 4.449u 0.401s 0:05.18 93.4% 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 8 2011 at 23:08:53 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 = 2423 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: 1.941324 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): -13.83800 41.17600 ymin,ymax (A): 12.44900 65.45600 zmin,zma (A): 3.136000 45.66000 x,y,z range (A): 55.01400 53.00700 42.52400 scale (grids/A): 1.941324 object centre (A): 13.66900 38.95250 24.39800 number of atom coordinates read : 2423 total number of charged atoms : 2287 net assigned charge : 12.00002 assigned positive charge : 354.8472 centred at (gu) : 89.79002 86.94003 87.36465 assigned negative charge : -342.8480 centred at (gu) : 89.93835 86.91795 87.61618 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22461 grid for indexing accessible points = 1.400000 m= 27450 mr = 49739 m= 5347 mr = 20139 m= 458 mr = 3537 m= 12 mr = 224 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.6200000 number of dielectric boundary points 33224 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 18020 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) : 0.6471080 object centre at (A) : 13.66900 38.95250 24.39800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6270063E-02 1.3913664E-03 midg,1,midg; midg,igrid,midg 2.5584849E-02 5.6611881E-02 1,midg,midg; igrid,midg,midg 5.9429605E-02 1.5569252E-02 gauss-seidel spectral radius is 0.9986755 estimated iterations to convergence 218 setup time was (sec) 0.9800000 now iterating at: 23:08:55 rms-change max change #iterations 4.119927 193.3468 at 10iterations 1.945648 77.65848 at 20iterations 0.9220381 30.29006 at 30iterations 0.4344539 14.40078 at 40iterations 0.2056917 8.103271 at 50iterations 9.7936913E-02 3.164991 at 60iterations 4.6199929E-02 1.410661 at 70iterations 2.1861974E-02 0.7032166 at 80iterations 1.0394419E-02 0.3451843 at 90iterations 4.9815346E-03 0.1629000 at 100iterations 2.4012132E-03 7.7339172E-02 at 110iterations 1.1859511E-03 4.0717840E-02 at 120iterations finished qdiffx linear iterations at : 23:09:05 total time elapsed so far: 10.79000 # loops : 120 mean,max change (kT/e) : 1.1859511E-03 4.0717840E-02 energy calculations done at 10.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.96000 DelPhi exited at 23:09:05 10.963u 0.423s 0:11.64 97.7% 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 Sat Oct 8 2011 at 23:09:05 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 = 2423 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: 2.911986 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): -13.83800 41.17600 ymin,ymax (A): 12.44900 65.45600 zmin,zma (A): 3.136000 45.66000 x,y,z range (A): 55.01400 53.00700 42.52400 scale (grids/A): 2.911986 object centre (A): 13.66900 38.95250 24.39800 number of atom coordinates read : 2423 total number of charged atoms : 2287 net assigned charge : 12.00002 assigned positive charge : 354.8472 centred at (gu) : 89.68488 85.40982 86.04688 assigned negative charge : -342.8480 centred at (gu) : 89.90758 85.37694 86.42437 start vw surface at 0.1200000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 169784 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22461 grid for indexing accessible points = 1.400000 m= 86218 mr = 120728 m= 34396 mr = 69813 m= 10184 mr = 28036 m= 1926 mr = 7890 m= 195 mr = 1356 m= 5 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 90 time to turn everything in is 1.640000 number of dielectric boundary points 74781 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 18296 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) : 1.941324 object centre at (A) : 13.66900 38.95250 24.39800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3440922 3.9334632E-03 midg,1,midg; midg,igrid,midg 0.2297606 0.7301407 1,midg,midg; igrid,midg,midg 0.5444995 8.3367676E-02 gauss-seidel spectral radius is 0.9992741 estimated iterations to convergence 293 setup time was (sec) 1.980000 now iterating at: 23:09:08 rms-change max change #iterations 9.737115 370.6611 at 10iterations 5.757663 135.3764 at 20iterations 3.384485 72.53831 at 30iterations 1.976850 41.51539 at 40iterations 1.153715 22.69092 at 50iterations 0.6721337 14.36829 at 60iterations 0.3910795 7.852455 at 70iterations 0.2275136 4.777061 at 80iterations 0.1320058 2.684565 at 90iterations 7.6718688E-02 1.394394 at 100iterations 4.4343986E-02 0.8344669 at 110iterations 2.5760077E-02 0.4774733 at 120iterations 1.4904493E-02 0.2855892 at 130iterations 8.6845485E-03 0.1750239 at 140iterations 5.0436775E-03 9.8373413E-02 at 150iterations 2.9504534E-03 6.3908577E-02 at 160iterations 1.7380245E-03 3.6338806E-02 at 170iterations 1.0439275E-03 2.3344040E-02 at 180iterations finished qdiffx linear iterations at : 23:09:24 total time elapsed so far: 18.92000 # loops : 180 mean,max change (kT/e) : 1.0439275E-03 2.3344040E-02 energy calculations done at 18.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.07000 DelPhi exited at 23:09:25 19.076u 0.465s 0:19.82 98.5% 0+0k 0+0io 0pf+0w