Sat Oct 15 13:46:12 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 15 2011 at 13:46:12 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 = 2318 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6717362 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): -3.322000 49.67500 ymin,ymax (A): 41.91600 88.64900 zmin,zma (A): -4.612000 41.60900 x,y,z range (A): 52.99700 46.73300 46.22100 scale (grids/A): 0.6717362 object centre (A): 23.17650 65.28250 18.49850 number of atom coordinates read : 2318 total number of charged atoms : 2219 net assigned charge : -0.9999951 assigned positive charge : 339.5872 centred at (gu) : 90.63971 90.86087 89.88457 assigned negative charge : -340.5879 centred at (gu) : 90.53927 90.97269 89.94965 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7164 nv = 96 ne = 84 npr = 47365 no. pairs analyzed = 47365 no. exposed pairs = 2895 no. arc points = 20424 no. surface atoms = 988 nbur = 1330 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 453 mr = 3967 m= 3 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3580 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1908 ## 138 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8364 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1986646E-08 -1.8210363E-08 midg,1,midg; midg,igrid,midg 1.8694367E-08 -3.5614523E-08 1,midg,midg; igrid,midg,midg -2.3685855E-08 2.2673268E-08 gauss-seidel spectral radius is 0.9884890 estimated iterations to convergence 76 setup time was (sec) 0.4200000 now iterating at: 13:46:13 rms-change max change #iterations 0.1643350 24.01490 at 10iterations 1.8230837E-02 2.465652 at 20iterations 1.9856163E-03 0.2921100 at 30iterations 2.2095676E-04 3.2966614E-02 at 40iterations 2.4991827E-05 4.2371750E-03 at 50iterations finished qdiffx linear iterations at : 13:46:16 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 2.4991827E-05 4.2371750E-03 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.920000 DelPhi exited at 13:46:17 3.921u 0.249s 0:04.48 92.8% 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 Sat Oct 15 2011 at 13:46:17 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 = 2318 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.015208 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): -3.322000 49.67500 ymin,ymax (A): 41.91600 88.64900 zmin,zma (A): -4.612000 41.60900 x,y,z range (A): 52.99700 46.73300 46.22100 scale (grids/A): 2.015208 object centre (A): 23.17650 65.28250 18.49850 number of atom coordinates read : 2318 total number of charged atoms : 2219 net assigned charge : -0.9999951 assigned positive charge : 339.5872 centred at (gu) : 91.91868 92.58212 89.65323 assigned negative charge : -340.5879 centred at (gu) : 91.61774 92.91809 89.84888 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20424 grid for indexing accessible points = 1.400000 m= 28461 mr = 53060 m= 5199 mr = 21080 m= 400 mr = 3307 m= 12 mr = 188 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1256 time to turn everything in is 0.4100000 number of dielectric boundary points 32788 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 99 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 17596 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) : 0.6717362 object centre at (A) : 23.17650 65.28250 18.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0085913E-04 -3.6538605E-02 midg,1,midg; midg,igrid,midg 1.9131089E-02 -4.3083075E-02 1,midg,midg; igrid,midg,midg 7.6843398E-03 6.7032672E-02 gauss-seidel spectral radius is 0.9987515 estimated iterations to convergence 224 setup time was (sec) 0.6800000 now iterating at: 13:46:18 rms-change max change #iterations 4.366541 208.7375 at 10iterations 2.112013 75.87471 at 20iterations 1.024760 30.70785 at 30iterations 0.4940765 16.13049 at 40iterations 0.2392303 6.828892 at 50iterations 0.1160657 4.076210 at 60iterations 5.6090292E-02 1.651361 at 70iterations 2.7108489E-02 0.8841658 at 80iterations 1.3164313E-02 0.4016705 at 90iterations 6.3615912E-03 0.2024903 at 100iterations 3.0911674E-03 9.9715233E-02 at 110iterations 1.4973402E-03 4.2991638E-02 at 120iterations finished qdiffx linear iterations at : 13:46:26 total time elapsed so far: 9.280000 # loops : 120 mean,max change (kT/e) : 1.4973402E-03 4.2991638E-02 energy calculations done at 9.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.420000 DelPhi exited at 13:46:27 9.427u 0.299s 0:10.05 96.6% 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 Sat Oct 15 2011 at 13:46:27 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 = 2318 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.022813 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): -3.322000 49.67500 ymin,ymax (A): 41.91600 88.64900 zmin,zma (A): -4.612000 41.60900 x,y,z range (A): 52.99700 46.73300 46.22100 scale (grids/A): 3.022813 object centre (A): 23.17650 65.28250 18.49850 number of atom coordinates read : 2318 total number of charged atoms : 2219 net assigned charge : -0.9999951 assigned positive charge : 339.5872 centred at (gu) : 92.87804 93.87317 89.47974 assigned negative charge : -340.5879 centred at (gu) : 92.42662 94.37716 89.77323 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 176651 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20424 grid for indexing accessible points = 1.400000 m= 89923 mr = 128764 m= 35375 mr = 73652 m= 9590 mr = 28563 m= 1654 mr = 7271 m= 159 mr = 1137 m= 5 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 4326 time to turn everything in is 1.100000 number of dielectric boundary points 73870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 17752 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) : 2.015208 object centre at (A) : 23.17650 65.28250 18.49850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7358709E-03 -0.2811665 midg,1,midg; midg,igrid,midg 0.2985498 -0.4317906 1,midg,midg; igrid,midg,midg 0.1519256 0.6815491 gauss-seidel spectral radius is 0.9992836 estimated iterations to convergence 295 setup time was (sec) 1.400000 now iterating at: 13:46:28 rms-change max change #iterations 10.04846 407.0266 at 10iterations 5.890893 118.0099 at 20iterations 3.455590 67.92854 at 30iterations 2.015298 39.83814 at 40iterations 1.178017 23.96582 at 50iterations 0.6865872 11.66498 at 60iterations 0.4004363 7.803309 at 70iterations 0.2330790 5.495152 at 80iterations 0.1356027 2.519545 at 90iterations 7.8728922E-02 1.313132 at 100iterations 4.5686439E-02 0.7605972 at 110iterations 2.6592100E-02 0.4716985 at 120iterations 1.5431792E-02 0.2567040 at 130iterations 8.9543397E-03 0.1679039 at 140iterations 5.1975064E-03 9.3372345E-02 at 150iterations 3.0126220E-03 5.4440975E-02 at 160iterations 1.7466035E-03 2.9775620E-02 at 170iterations 1.0139947E-03 1.7490387E-02 at 180iterations finished qdiffx linear iterations at : 13:46:53 total time elapsed so far: 15.23000 # loops : 180 mean,max change (kT/e) : 1.0139947E-03 1.7490387E-02 energy calculations done at 15.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.35000 DelPhi exited at 13:46:55 15.352u 0.335s 0:27.88 56.2% 0+0k 0+0io 0pf+0w