Thu Feb 2 03:20:47 PST 2012 #!/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 Thu Feb 2 2012 at 03:20:47 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2466 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: 0.6746001 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): -22.27700 27.31300 ymin,ymax (A): 3.700000 44.70200 zmin,zma (A): -2.500000 50.27200 x,y,z range (A): 49.59000 41.00200 52.77200 scale (grids/A): 0.6746001 object centre (A): 2.518000 24.20100 23.88600 number of atom coordinates read : 2466 total number of charged atoms : 2332 net assigned charge : 8.7916851E-06 assigned positive charge : 359.8650 centred at (gu) : 90.68784 90.84158 90.77227 assigned negative charge : -359.8660 centred at (gu) : 90.62422 90.79726 90.78636 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7725 nv = 96 ne = 84 npr = 50436 no. pairs analyzed = 50436 no. exposed pairs = 3261 no. arc points = 22447 no. surface atoms = 1095 nbur = 1371 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 457 mr = 4191 m= 3 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2100000 number of dielectric boundary points 3926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2056 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8811 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9948255E-09 -4.6214801E-09 midg,1,midg; midg,igrid,midg -1.0052832E-08 1.3663077E-08 1,midg,midg; igrid,midg,midg -1.4844739E-08 1.9046212E-08 gauss-seidel spectral radius is 0.9886021 estimated iterations to convergence 76 setup time was (sec) 0.4000000 now iterating at: 03:20:48 rms-change max change #iterations 0.1754873 26.50087 at 10iterations 1.9766722E-02 2.780777 at 20iterations 2.2401775E-03 0.3039589 at 30iterations 2.7654675E-04 3.7247658E-02 at 40iterations 4.5052751E-05 6.0405731E-03 at 50iterations finished qdiffx linear iterations at : 03:20:51 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 4.5052751E-05 6.0405731E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 03:20:51 3.484u 0.224s 0:04.02 92.0% 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 Thu Feb 2 2012 at 03:20:51 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2466 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: 2.023800 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): -22.27700 27.31300 ymin,ymax (A): 3.700000 44.70200 zmin,zma (A): -2.500000 50.27200 x,y,z range (A): 49.59000 41.00200 52.77200 scale (grids/A): 2.023800 object centre (A): 2.518000 24.20100 23.88600 number of atom coordinates read : 2466 total number of charged atoms : 2332 net assigned charge : 8.7916851E-06 assigned positive charge : 359.8650 centred at (gu) : 92.06297 92.52424 92.31648 assigned negative charge : -359.8660 centred at (gu) : 91.87270 92.39168 92.35933 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82444 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22447 grid for indexing accessible points = 1.400000 m= 30361 mr = 56838 m= 5431 mr = 21928 m= 450 mr = 3441 m= 7 mr = 218 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 974 time to turn everything in is 0.4200000 number of dielectric boundary points 36268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 18463 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) : 0.6746001 object centre at (A) : 2.518000 24.20100 23.88600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0928887E-02 1.2101548E-02 midg,1,midg; midg,igrid,midg -2.0129191E-02 3.5772885E-03 1,midg,midg; igrid,midg,midg 1.1232190E-02 1.5727790E-02 gauss-seidel spectral radius is 0.9987777 estimated iterations to convergence 226 setup time was (sec) 0.6500000 now iterating at: 03:20:52 rms-change max change #iterations 4.593237 203.0109 at 10iterations 2.229152 72.38721 at 20iterations 1.082929 31.41291 at 30iterations 0.5277540 16.89332 at 40iterations 0.2570407 7.794019 at 50iterations 0.1256550 3.601549 at 60iterations 6.1260879E-02 1.819044 at 70iterations 2.9847581E-02 0.8215160 at 80iterations 1.4530434E-02 0.4019251 at 90iterations 7.0893290E-03 0.2273979 at 100iterations 3.4827504E-03 9.7757578E-02 at 110iterations 1.7164801E-03 5.0735474E-02 at 120iterations finished qdiffx linear iterations at : 03:21:00 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 1.7164801E-03 5.0735474E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 03:21:00 8.062u 0.209s 0:08.64 95.6% 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 Thu Feb 2 2012 at 03:21:00 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2466 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: 3.035701 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): -22.27700 27.31300 ymin,ymax (A): 3.700000 44.70200 zmin,zma (A): -2.500000 50.27200 x,y,z range (A): 49.59000 41.00200 52.77200 scale (grids/A): 3.035701 object centre (A): 2.518000 24.20100 23.88600 number of atom coordinates read : 2466 total number of charged atoms : 2332 net assigned charge : 8.7916851E-06 assigned positive charge : 359.8650 centred at (gu) : 93.09435 93.78630 93.47448 assigned negative charge : -359.8660 centred at (gu) : 92.80905 93.58753 93.53904 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 190678 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22447 grid for indexing accessible points = 1.400000 m= 96245 mr = 137943 m= 37071 mr = 77912 m= 9968 mr = 29485 m= 1855 mr = 7520 m= 174 mr = 1318 m= 3 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.6299999 no. cavity mid-points inaccessible to solvent = 3023 time to turn everything in is 1.090000 number of dielectric boundary points 81716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 18656 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) : 2.023800 object centre at (A) : 2.518000 24.20100 23.88600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5925542E-02 5.1119115E-02 midg,1,midg; midg,igrid,midg -0.2152519 -4.3498322E-02 1,midg,midg; igrid,midg,midg 0.3051584 0.2224581 gauss-seidel spectral radius is 0.9993017 estimated iterations to convergence 299 setup time was (sec) 1.330000 now iterating at: 03:21:02 rms-change max change #iterations 10.57812 527.7136 at 10iterations 6.269026 127.7233 at 20iterations 3.715685 67.91235 at 30iterations 2.189984 38.16076 at 40iterations 1.290370 22.41579 at 50iterations 0.7579578 12.88123 at 60iterations 0.4451155 8.213936 at 70iterations 0.2610524 5.012276 at 80iterations 0.1529929 2.700658 at 90iterations 8.9374341E-02 1.483749 at 100iterations 5.2294713E-02 0.9080315 at 110iterations 3.0632030E-02 0.5323105 at 120iterations 1.7948244E-02 0.3147743 at 130iterations 1.0518722E-02 0.1773500 at 140iterations 6.1739534E-03 0.1107664 at 150iterations 3.6449959E-03 6.1395645E-02 at 160iterations 2.1711902E-03 3.7458904E-02 at 170iterations 1.3116995E-03 2.4251938E-02 at 180iterations finished qdiffx linear iterations at : 03:21:13 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 1.3116995E-03 2.4251938E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 03:21:14 13.031u 0.253s 0:13.57 97.8% 0+0k 0+0io 0pf+0w