Sun Oct 9 13:20:10 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 Sun Oct 9 2011 at 13:20:10 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2389 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6972600 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): -6.717000 44.34000 ymin,ymax (A): 22.08300 72.85000 zmin,zma (A): 41.85300 85.46301 x,y,z range (A): 51.05700 50.76700 43.61001 scale (grids/A): 0.6972600 object centre (A): 18.81150 47.46650 63.65800 number of atom coordinates read : 2389 total number of charged atoms : 2248 net assigned charge : 3.500020 assigned positive charge : 366.3021 centred at (gu) : 89.70466 91.32712 90.26620 assigned negative charge : -362.8026 centred at (gu) : 89.72450 91.50673 90.32826 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7908 nv = 96 ne = 84 npr = 47882 no. pairs analyzed = 47882 no. exposed pairs = 2985 no. arc points = 21118 no. surface atoms = 1003 nbur = 1386 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 533 mr = 4438 m= 1 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3920 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1926 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8877 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9884228E-08 -4.2966670E-09 midg,1,midg; midg,igrid,midg 8.0620154E-08 -7.7716720E-08 1,midg,midg; igrid,midg,midg 3.5466307E-08 1.4586324E-08 gauss-seidel spectral radius is 0.9893157 estimated iterations to convergence 79 setup time was (sec) 0.5000000 now iterating at: 13:20:10 rms-change max change #iterations 0.2060126 30.15894 at 10iterations 2.5048312E-02 3.502258 at 20iterations 3.7336343E-03 0.4725418 at 30iterations 9.1365719E-04 0.1534004 at 40iterations 3.1422588E-04 5.0392151E-02 at 50iterations finished qdiffx linear iterations at : 13:20:13 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 3.1422588E-04 5.0392151E-02 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 13:20:13 3.105u 0.115s 0:03.51 91.4% 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 Sun Oct 9 2011 at 13:20:13 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2389 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: 2.091780 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): -6.717000 44.34000 ymin,ymax (A): 22.08300 72.85000 zmin,zma (A): 41.85300 85.46301 x,y,z range (A): 51.05700 50.76700 43.61001 scale (grids/A): 2.091780 object centre (A): 18.81150 47.46650 63.65800 number of atom coordinates read : 2389 total number of charged atoms : 2248 net assigned charge : 3.500020 assigned positive charge : 366.3021 centred at (gu) : 89.11356 93.98096 90.79829 assigned negative charge : -362.8026 centred at (gu) : 89.17334 94.52011 90.98453 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 83904 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21118 grid for indexing accessible points = 1.400000 m= 32890 mr = 58453 m= 6255 mr = 24717 m= 607 mr = 4087 m= 13 mr = 323 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 36089 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 17832 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) : 0.6972600 object centre at (A) : 18.81150 47.46650 63.65800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4144179E-02 -4.2341740E-04 midg,1,midg; midg,igrid,midg 1.4250233E-02 -6.8611540E-02 1,midg,midg; igrid,midg,midg 6.6693537E-02 -1.0610067E-02 gauss-seidel spectral radius is 0.9988410 estimated iterations to convergence 232 setup time was (sec) 0.8600000 now iterating at: 13:20:14 rms-change max change #iterations 5.004588 221.4198 at 10iterations 2.477749 85.57407 at 20iterations 1.232888 40.70476 at 30iterations 0.6119551 18.15811 at 40iterations 0.3046398 9.269041 at 50iterations 0.1515475 4.551167 at 60iterations 7.5799599E-02 2.478321 at 70iterations 3.7899576E-02 1.104115 at 80iterations 1.9058563E-02 0.5354919 at 90iterations 9.7149322E-03 0.2608566 at 100iterations 5.0422242E-03 0.1603241 at 110iterations 2.7438893E-03 8.7459564E-02 at 120iterations finished qdiffx linear iterations at : 13:20:20 total time elapsed so far: 6.740000 # loops : 120 mean,max change (kT/e) : 2.7438893E-03 8.7459564E-02 energy calculations done at 6.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.920000 DelPhi exited at 13:20:21 6.920u 0.152s 0:07.37 95.9% 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 Sun Oct 9 2011 at 13:20:21 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2389 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: 3.137670 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): -6.717000 44.34000 ymin,ymax (A): 22.08300 72.85000 zmin,zma (A): 41.85300 85.46301 x,y,z range (A): 51.05700 50.76700 43.61001 scale (grids/A): 3.137670 object centre (A): 18.81150 47.46650 63.65800 number of atom coordinates read : 2389 total number of charged atoms : 2248 net assigned charge : 3.500020 assigned positive charge : 366.3021 centred at (gu) : 88.67029 95.97148 91.19717 assigned negative charge : -362.8026 centred at (gu) : 88.75996 96.77986 91.47675 start vw surface at 0.1400000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 193228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21118 grid for indexing accessible points = 1.400000 m= 102564 mr = 140767 m= 41652 mr = 84708 m= 11665 mr = 34079 m= 2486 mr = 8955 m= 311 mr = 1793 m= 7 mr = 189 m= 0 mr = 2 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.850000 number of dielectric boundary points 81420 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 17984 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) : 2.091780 object centre at (A) : 18.81150 47.46650 63.65800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5972913 -0.1413291 midg,1,midg; midg,igrid,midg 0.3277621 -0.7425296 1,midg,midg; igrid,midg,midg 0.7101662 -0.4034449 gauss-seidel spectral radius is 0.9993036 estimated iterations to convergence 299 setup time was (sec) 2.120000 now iterating at: 13:20:23 rms-change max change #iterations 11.06509 407.1577 at 10iterations 6.563324 158.4365 at 20iterations 3.876327 76.23151 at 30iterations 2.290404 52.51242 at 40iterations 1.351770 22.21244 at 50iterations 0.7947669 14.38328 at 60iterations 0.4678352 8.311401 at 70iterations 0.2748826 4.626229 at 80iterations 0.1612301 2.784718 at 90iterations 9.4923556E-02 1.582183 at 100iterations 5.5780437E-02 0.9081402 at 110iterations 3.3014003E-02 0.5213203 at 120iterations 1.9724792E-02 0.3486872 at 130iterations 1.2006294E-02 0.2055969 at 140iterations 7.5572585E-03 0.1409912 at 150iterations 4.9844249E-03 9.5779419E-02 at 160iterations 3.4890098E-03 7.3135376E-02 at 170iterations 2.6214917E-03 5.9864044E-02 at 180iterations finished qdiffx linear iterations at : 13:20:32 total time elapsed so far: 11.54000 # loops : 180 mean,max change (kT/e) : 2.6214917E-03 5.9864044E-02 energy calculations done at 11.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 13:20:33 11.718u 0.155s 0:12.14 97.6% 0+0k 0+0io 0pf+0w