Sun Oct 9 23:46:26 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 23:46:26 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 = 3133 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5948303 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): -29.30700 30.54200 ymin,ymax (A): 7.945000 61.80400 zmin,zma (A): 24.92800 77.25300 x,y,z range (A): 59.84900 53.85900 52.32500 scale (grids/A): 0.5948303 object centre (A): 0.6175003 34.87450 51.09050 number of atom coordinates read : 3133 total number of charged atoms : 2988 net assigned charge : -0.4999911 assigned positive charge : 470.1989 centred at (gu) : 89.72531 89.06259 89.00607 assigned negative charge : -470.7002 centred at (gu) : 89.78249 89.07405 89.11732 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7399 nv = 96 ne = 84 npr = 62331 no. pairs analyzed = 62331 no. exposed pairs = 4079 no. arc points = 28991 no. surface atoms = 1355 nbur = 1778 mkacc time = 0.1400000 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 = 1.456000 m= 342 mr = 3892 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3700000 number of dielectric boundary points 3833 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2880 ## 325 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9323 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9183853E-09 -3.5544525E-09 midg,1,midg; midg,igrid,midg 2.4535818E-10 -5.3828181E-10 1,midg,midg; igrid,midg,midg 2.0271087E-09 -2.2520337E-09 gauss-seidel spectral radius is 0.9854257 estimated iterations to convergence 68 setup time was (sec) 0.5900000 now iterating at: 23:46:27 rms-change max change #iterations 0.1154228 17.32614 at 10iterations 9.6701048E-03 1.444225 at 20iterations 7.9281669E-04 0.1144829 at 30iterations 7.1634604E-05 1.0463715E-02 at 40iterations 8.6804330E-06 1.1520386E-03 at 50iterations finished qdiffx linear iterations at : 23:46:29 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 8.6804330E-06 1.1520386E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 23:46:30 3.404u 0.186s 0:03.96 90.4% 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 23:46:30 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 = 3133 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.784491 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): -29.30700 30.54200 ymin,ymax (A): 7.945000 61.80400 zmin,zma (A): 24.92800 77.25300 x,y,z range (A): 59.84900 53.85900 52.32500 scale (grids/A): 1.784491 object centre (A): 0.6175003 34.87450 51.09050 number of atom coordinates read : 3133 total number of charged atoms : 2988 net assigned charge : -0.4999911 assigned positive charge : 470.1989 centred at (gu) : 89.17509 87.18687 87.01756 assigned negative charge : -470.7002 centred at (gu) : 89.34687 87.22202 87.35196 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81037 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28991 grid for indexing accessible points = 1.400000 m= 26005 mr = 55232 m= 3141 mr = 18059 m= 92 mr = 1661 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1588 time to turn everything in is 0.5900000 number of dielectric boundary points 35319 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 23303 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) : 0.5948303 object centre at (A) : 0.6175003 34.87450 51.09050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0626687E-02 -5.5935951E-03 midg,1,midg; midg,igrid,midg 7.8176381E-03 6.0771550E-03 1,midg,midg; igrid,midg,midg 1.4596113E-02 -1.2391731E-02 gauss-seidel spectral radius is 0.9985154 estimated iterations to convergence 206 setup time was (sec) 0.8700000 now iterating at: 23:46:31 rms-change max change #iterations 4.165407 159.2326 at 10iterations 1.873001 67.26573 at 20iterations 0.8480526 29.29392 at 30iterations 0.3841129 13.85477 at 40iterations 0.1739331 5.480655 at 50iterations 7.8914471E-02 2.394562 at 60iterations 3.5613038E-02 1.148949 at 70iterations 1.6142370E-02 0.5352211 at 80iterations 7.3264525E-03 0.2503204 at 90iterations 3.3266481E-03 0.1084499 at 100iterations 1.5092415E-03 5.2232742E-02 at 110iterations 6.8505312E-04 2.1644592E-02 at 120iterations finished qdiffx linear iterations at : 23:46:38 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 6.8505312E-04 2.1644592E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 23:46:38 7.581u 0.176s 0:08.03 96.5% 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 23:46:38 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 = 3133 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.676737 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): -29.30700 30.54200 ymin,ymax (A): 7.945000 61.80400 zmin,zma (A): 24.92800 77.25300 x,y,z range (A): 59.84900 53.85900 52.32500 scale (grids/A): 2.676737 object centre (A): 0.6175003 34.87450 51.09050 number of atom coordinates read : 3133 total number of charged atoms : 2988 net assigned charge : -0.4999911 assigned positive charge : 470.1989 centred at (gu) : 88.76242 85.77998 85.52599 assigned negative charge : -470.7002 centred at (gu) : 89.02018 85.83290 86.02789 start vw surface at 0.2100000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 188152 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28991 grid for indexing accessible points = 1.400000 m= 88132 mr = 134691 m= 27024 mr = 70184 m= 5154 mr = 20588 m= 473 mr = 3516 m= 10 mr = 248 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 5286 time to turn everything in is 1.480000 number of dielectric boundary points 79718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 23899 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) : 1.784491 object centre at (A) : 0.6175003 34.87450 51.09050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1551328 -3.6524833E-04 midg,1,midg; midg,igrid,midg 7.1230210E-02 0.1093115 1,midg,midg; igrid,midg,midg 0.1760288 -0.1291043 gauss-seidel spectral radius is 0.9992477 estimated iterations to convergence 288 setup time was (sec) 1.780000 now iterating at: 23:46:40 rms-change max change #iterations 10.19199 331.4673 at 10iterations 6.014607 161.4249 at 20iterations 3.517591 81.92986 at 30iterations 2.047956 43.72024 at 40iterations 1.187498 22.78492 at 50iterations 0.6856291 14.85627 at 60iterations 0.3971740 7.539752 at 70iterations 0.2289940 4.489706 at 80iterations 0.1316586 2.735369 at 90iterations 7.5781234E-02 1.373931 at 100iterations 4.3469593E-02 1.037720 at 110iterations 2.4935709E-02 0.4477191 at 120iterations 1.4309428E-02 0.2693092 at 130iterations 8.2291998E-03 0.1720685 at 140iterations 4.7126077E-03 8.7877274E-02 at 150iterations 2.6966545E-03 5.6525230E-02 at 160iterations 1.5436455E-03 2.8047562E-02 at 170iterations 8.8414282E-04 1.6347885E-02 at 180iterations finished qdiffx linear iterations at : 23:46:51 total time elapsed so far: 12.42000 # loops : 180 mean,max change (kT/e) : 8.8414282E-04 1.6347885E-02 energy calculations done at 12.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 23:46:51 12.658u 0.186s 0:13.14 97.6% 0+0k 0+0io 0pf+0w