Sun Oct 9 22:49:18 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 Sun Oct 9 2011 at 22:49:18 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 = 4251 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: 0.5268376 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): 35.62800 99.66100 ymin,ymax (A): -20.64600 46.92700 zmin,zma (A): 18.61300 71.39600 x,y,z range (A): 64.03300 67.57300 52.78300 scale (grids/A): 0.5268376 object centre (A): 67.64450 13.14050 45.00450 number of atom coordinates read : 4251 total number of charged atoms : 4094 net assigned charge : 3.000012 assigned positive charge : 644.1456 centred at (gu) : 90.23685 91.21262 89.45422 assigned negative charge : -641.1493 centred at (gu) : 90.26184 91.29159 89.52100 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7668 nv = 96 ne = 84 npr = 83534 no. pairs analyzed = 83534 no. exposed pairs = 5518 no. arc points = 39123 no. surface atoms = 1858 nbur = 2393 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 287 mr = 3934 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4017 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3847 ## 545 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 10194 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5020004E-10 -1.8835514E-10 midg,1,midg; midg,igrid,midg 3.2664413E-10 -3.7852763E-10 1,midg,midg; igrid,midg,midg 1.9095003E-10 -2.6690013E-11 gauss-seidel spectral radius is 0.9815402 estimated iterations to convergence 61 setup time was (sec) 0.4800000 now iterating at: 22:49:19 rms-change max change #iterations 7.1017280E-02 11.70999 at 10iterations 4.4273492E-03 0.6799927 at 20iterations 3.1739031E-04 4.7458649E-02 at 30iterations 6.1070212E-05 1.3327360E-02 at 40iterations 2.0708829E-05 4.6696663E-03 at 50iterations finished qdiffx linear iterations at : 22:49:22 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 2.0708829E-05 4.6696663E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 22:49:22 3.546u 0.174s 0:04.15 89.3% 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 22:49:22 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 = 4251 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: 1.580513 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): 35.62800 99.66100 ymin,ymax (A): -20.64600 46.92700 zmin,zma (A): 18.61300 71.39600 x,y,z range (A): 64.03300 67.57300 52.78300 scale (grids/A): 1.580513 object centre (A): 67.64450 13.14050 45.00450 number of atom coordinates read : 4251 total number of charged atoms : 4094 net assigned charge : 3.000012 assigned positive charge : 644.1456 centred at (gu) : 90.70880 93.63644 88.36125 assigned negative charge : -641.1493 centred at (gu) : 90.78535 93.87405 88.56260 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 86237 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39123 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 25768 mr = 58389 m= 2403 mr = 17552 m= 50 mr = 1157 m= 0 mr = 2 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 37358 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 523 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 31114 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) : 0.5268376 object centre at (A) : 67.64450 13.14050 45.00450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7304244E-03 -9.3402332E-03 midg,1,midg; midg,igrid,midg 2.9263476E-02 -1.7029407E-03 1,midg,midg; igrid,midg,midg 1.3246623E-02 1.5816662E-02 gauss-seidel spectral radius is 0.9981962 estimated iterations to convergence 187 setup time was (sec) 0.6400000 now iterating at: 22:49:23 rms-change max change #iterations 3.776071 150.8825 at 10iterations 1.572904 50.02374 at 20iterations 0.6572302 22.02677 at 30iterations 0.2749495 9.251699 at 40iterations 0.1148691 3.649453 at 50iterations 4.7945041E-02 1.579445 at 60iterations 2.0057140E-02 0.6682339 at 70iterations 8.4032509E-03 0.2559901 at 80iterations 3.5310907E-03 0.1085749 at 90iterations 1.4880066E-03 4.5623779E-02 at 100iterations 6.3942070E-04 2.1204948E-02 at 110iterations 2.8259406E-04 9.0856552E-03 at 120iterations finished qdiffx linear iterations at : 22:49:30 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 2.8259406E-04 9.0856552E-03 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 22:49:31 8.000u 0.211s 0:08.52 96.3% 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 22:49:31 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 = 4251 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: 2.370770 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): 35.62800 99.66100 ymin,ymax (A): -20.64600 46.92700 zmin,zma (A): 18.61300 71.39600 x,y,z range (A): 64.03300 67.57300 52.78300 scale (grids/A): 2.370770 object centre (A): 67.64450 13.14050 45.00450 number of atom coordinates read : 4251 total number of charged atoms : 4094 net assigned charge : 3.000012 assigned positive charge : 644.1456 centred at (gu) : 91.06300 95.45428 87.54150 assigned negative charge : -641.1493 centred at (gu) : 91.17796 95.81086 87.84364 start vw surface at 0.1200000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 200580 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39123 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 91004 mr = 143393 m= 24340 mr = 71541 m= 3458 mr = 17964 m= 188 mr = 2255 m= 1 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.030000 number of dielectric boundary points 84334 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 32682 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) : 1.580513 object centre at (A) : 67.64450 13.14050 45.00450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5082121E-02 -0.1369801 midg,1,midg; midg,igrid,midg 0.4042623 -0.3109649 1,midg,midg; igrid,midg,midg 0.3119823 0.3865245 gauss-seidel spectral radius is 0.9991782 estimated iterations to convergence 275 setup time was (sec) 1.280000 now iterating at: 22:49:32 rms-change max change #iterations 10.20781 258.4144 at 10iterations 5.939678 146.7787 at 20iterations 3.416511 75.09861 at 30iterations 1.954086 40.20974 at 40iterations 1.113507 28.33666 at 50iterations 0.6301542 12.78984 at 60iterations 0.3564402 8.392668 at 70iterations 0.2006283 3.621307 at 80iterations 0.1128748 2.003787 at 90iterations 6.3401148E-02 1.180550 at 100iterations 3.5582375E-02 0.7488346 at 110iterations 1.9938957E-02 0.3942196 at 120iterations 1.1178732E-02 0.2006931 at 130iterations 6.2606260E-03 0.1150379 at 140iterations 3.5107553E-03 6.7100525E-02 at 150iterations 1.9731226E-03 3.6558151E-02 at 160iterations 1.1176456E-03 1.9862175E-02 at 170iterations 6.3676632E-04 1.1082530E-02 at 180iterations finished qdiffx linear iterations at : 22:49:44 total time elapsed so far: 12.84000 # loops : 180 mean,max change (kT/e) : 6.3676632E-04 1.1082530E-02 energy calculations done at 12.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.97000 DelPhi exited at 22:49:44 12.973u 0.205s 0:13.53 97.3% 0+0k 0+0io 0pf+0w