Tue Oct 11 05:27:53 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 05:27:53 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1986 !!! 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: 0.7302714 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): -3.891000 44.85800 ymin,ymax (A): -22.31200 24.40800 zmin,zma (A): 5.566000 48.21200 x,y,z range (A): 48.74900 46.72000 42.64600 scale (grids/A): 0.7302714 object centre (A): 20.48350 1.048000 26.88900 number of atom coordinates read : 1986 total number of charged atoms : 1927 net assigned charge : 7.025011 assigned positive charge : 313.9671 centred at (gu) : 90.97209 89.18530 89.63712 assigned negative charge : -306.9421 centred at (gu) : 90.83759 89.32150 89.57429 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7500 nv = 96 ne = 84 npr = 37723 no. pairs analyzed = 37723 no. exposed pairs = 2570 no. arc points = 17639 no. surface atoms = 869 nbur = 1117 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 561 mr = 4281 m= 3 mr = 134 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 0.2900000 number of dielectric boundary points 3649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1606 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8060 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0811742E-08 1.3818371E-07 midg,1,midg; midg,igrid,midg 2.3932824E-07 -9.2205550E-09 1,midg,midg; igrid,midg,midg -7.6378717E-09 2.4501895E-07 gauss-seidel spectral radius is 0.9902163 estimated iterations to convergence 82 setup time was (sec) 0.5700000 now iterating at: 05:27:54 rms-change max change #iterations 0.2278038 32.27240 at 10iterations 2.9941760E-02 4.110672 at 20iterations 4.0661683E-03 0.5832932 at 30iterations 6.1711087E-04 8.7828636E-02 at 40iterations 1.2796998E-04 1.8678665E-02 at 50iterations finished qdiffx linear iterations at : 05:27:58 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 1.2796998E-04 1.8678665E-02 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 05:27:58 4.079u 0.264s 0:04.81 90.0% 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 05:27:58 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1986 !!! 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: 2.190814 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): -3.891000 44.85800 ymin,ymax (A): -22.31200 24.40800 zmin,zma (A): 5.566000 48.21200 x,y,z range (A): 48.74900 46.72000 42.64600 scale (grids/A): 2.190814 object centre (A): 20.48350 1.048000 26.88900 number of atom coordinates read : 1986 total number of charged atoms : 1927 net assigned charge : 7.025011 assigned positive charge : 313.9671 centred at (gu) : 92.91628 87.55637 88.91138 assigned negative charge : -306.9421 centred at (gu) : 92.51276 87.96465 88.72315 start vw surface at 0.1500000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 78970 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17639 grid for indexing accessible points = 1.400000 m= 33638 mr = 55767 m= 6995 mr = 25756 m= 719 mr = 4784 m= 26 mr = 394 m= 0 mr = 2 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 33645 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 15316 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) : 0.7302714 object centre at (A) : 20.48350 1.048000 26.88900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6310394E-02 2.8567361E-02 midg,1,midg; midg,igrid,midg 5.2149184E-02 -4.8067912E-02 1,midg,midg; igrid,midg,midg 4.1332513E-02 0.1062192 gauss-seidel spectral radius is 0.9988902 estimated iterations to convergence 238 setup time was (sec) 1.060000 now iterating at: 05:28:00 rms-change max change #iterations 4.868411 187.6770 at 10iterations 2.444794 88.83130 at 20iterations 1.243186 36.20799 at 30iterations 0.6271143 18.43432 at 40iterations 0.3160987 9.165174 at 50iterations 0.1601210 5.148933 at 60iterations 8.0758989E-02 2.332436 at 70iterations 4.0954784E-02 1.233386 at 80iterations 2.0705959E-02 0.6053123 at 90iterations 1.0491910E-02 0.3304882 at 100iterations 5.3384672E-03 0.1569061 at 110iterations 2.7344315E-03 7.8514099E-02 at 120iterations finished qdiffx linear iterations at : 05:28:08 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 2.7344315E-03 7.8514099E-02 energy calculations done at 9.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.720000 DelPhi exited at 05:28:09 9.725u 0.291s 0:10.62 94.2% 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 Tue Oct 11 2011 at 05:28:09 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1986 !!! 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: 3.286221 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): -3.891000 44.85800 ymin,ymax (A): -22.31200 24.40800 zmin,zma (A): 5.566000 48.21200 x,y,z range (A): 48.74900 46.72000 42.64600 scale (grids/A): 3.286221 object centre (A): 20.48350 1.048000 26.88900 number of atom coordinates read : 1986 total number of charged atoms : 1927 net assigned charge : 7.025011 assigned positive charge : 313.9671 centred at (gu) : 94.37436 86.33447 88.36713 assigned negative charge : -306.9421 centred at (gu) : 93.76924 86.94707 88.08487 start vw surface at 0.1400000 fill in re-entrant regions at 1.000000 boundary points on vw surface= 181457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17639 grid for indexing accessible points = 1.400000 m= 102718 mr = 134125 m= 44528 mr = 85713 m= 13391 mr = 36837 m= 2893 mr = 10592 m= 412 mr = 2108 m= 21 mr = 276 m= 0 mr = 4 time to grow re-entrant surface = 1.260000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.400000 number of dielectric boundary points 75765 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.550000 number of grid points assigned charge 15416 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) : 2.190814 object centre at (A) : 20.48350 1.048000 26.88900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1298255 0.1582752 midg,1,midg; midg,igrid,midg 0.4761263 -0.5239159 1,midg,midg; igrid,midg,midg 0.2310294 0.7591029 gauss-seidel spectral radius is 0.9993245 estimated iterations to convergence 303 setup time was (sec) 2.730000 now iterating at: 05:28:12 rms-change max change #iterations 10.71263 293.4672 at 10iterations 6.448951 161.9084 at 20iterations 3.872559 76.70377 at 30iterations 2.322056 45.87288 at 40iterations 1.387259 26.05469 at 50iterations 0.8258411 15.73271 at 60iterations 0.4908935 8.532706 at 70iterations 0.2915294 5.580179 at 80iterations 0.1730380 3.210338 at 90iterations 0.1026665 1.948387 at 100iterations 6.0840428E-02 1.067284 at 110iterations 3.6193181E-02 0.6345062 at 120iterations 2.1573963E-02 0.3969507 at 130iterations 1.2907571E-02 0.2281799 at 140iterations 7.8219697E-03 0.1598272 at 150iterations 4.8573101E-03 8.9141846E-02 at 160iterations 3.1089087E-03 5.5751801E-02 at 170iterations 2.0917894E-03 3.5838127E-02 at 180iterations finished qdiffx linear iterations at : 05:28:26 total time elapsed so far: 16.89000 # loops : 180 mean,max change (kT/e) : 2.0917894E-03 3.5838127E-02 energy calculations done at 16.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.08000 DelPhi exited at 05:28:27 17.079u 0.324s 0:17.85 97.4% 0+0k 0+0io 0pf+0w