Tue Oct 11 04:52:36 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 Tue Oct 11 2011 at 04:52:36 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 = 2089 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7225345 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): 1.591000 45.94400 ymin,ymax (A): 0.5260001 41.45800 zmin,zma (A): -2.220000 47.05100 x,y,z range (A): 44.35300 40.93200 49.27100 scale (grids/A): 0.7225345 object centre (A): 23.76750 20.99200 22.41550 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 90.97612 90.33759 90.55222 assigned negative charge : -311.0742 centred at (gu) : 91.10930 90.32500 90.63208 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7348 nv = 96 ne = 84 npr = 42617 no. pairs analyzed = 42617 no. exposed pairs = 2480 no. arc points = 16862 no. surface atoms = 848 nbur = 1241 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 536 mr = 4291 m= 4 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3511 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1590 ## 128 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8086 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2017851E-07 2.6170902E-08 midg,1,midg; midg,igrid,midg 6.6256945E-08 9.3400978E-08 1,midg,midg; igrid,midg,midg 1.4056556E-07 -1.7222002E-08 gauss-seidel spectral radius is 0.9900090 estimated iterations to convergence 81 setup time was (sec) 0.4900000 now iterating at: 04:52:37 rms-change max change #iterations 0.2162292 35.17284 at 10iterations 2.8326152E-02 3.829994 at 20iterations 3.8009698E-03 0.4576321 at 30iterations 6.2395079E-04 7.9786301E-02 at 40iterations 1.5346482E-04 2.1900177E-02 at 50iterations finished qdiffx linear iterations at : 04:52:40 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 1.5346482E-04 2.1900177E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 04:52:41 3.317u 0.199s 0:04.06 86.2% 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 04:52:41 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 = 2089 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: 2.167603 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): 1.591000 45.94400 ymin,ymax (A): 0.5260001 41.45800 zmin,zma (A): -2.220000 47.05100 x,y,z range (A): 44.35300 40.93200 49.27100 scale (grids/A): 2.167603 object centre (A): 23.76750 20.99200 22.41550 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 92.92838 91.01270 91.65672 assigned negative charge : -311.0742 centred at (gu) : 93.32784 90.97502 91.89634 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16862 grid for indexing accessible points = 1.400000 m= 32042 mr = 56039 m= 6397 mr = 24463 m= 530 mr = 4205 m= 7 mr = 232 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 32038 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 15574 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) : 0.7225345 object centre at (A) : 23.76750 20.99200 22.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9470756E-02 8.4923439E-02 midg,1,midg; midg,igrid,midg 3.8382423E-03 3.1443801E-02 1,midg,midg; igrid,midg,midg 3.1208031E-02 1.8050889E-02 gauss-seidel spectral radius is 0.9988704 estimated iterations to convergence 235 setup time was (sec) 0.8800000 now iterating at: 04:52:42 rms-change max change #iterations 4.762268 197.2567 at 10iterations 2.384403 85.54227 at 20iterations 1.203680 34.62748 at 30iterations 0.6042302 18.34952 at 40iterations 0.3051064 9.052574 at 50iterations 0.1533430 4.322495 at 60iterations 7.7207200E-02 2.192554 at 70iterations 3.8696766E-02 1.198326 at 80iterations 1.9453855E-02 0.6148627 at 90iterations 9.8694582E-03 0.2737741 at 100iterations 4.9644923E-03 0.1438370 at 110iterations 2.5323667E-03 6.8481445E-02 at 120iterations finished qdiffx linear iterations at : 04:52:48 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 2.5323667E-03 6.8481445E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 04:52:49 7.737u 0.220s 0:08.43 94.3% 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 Tue Oct 11 2011 at 04:52:49 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 = 2089 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.251405 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): 1.591000 45.94400 ymin,ymax (A): 0.5260001 41.45800 zmin,zma (A): -2.220000 47.05100 x,y,z range (A): 44.35300 40.93200 49.27100 scale (grids/A): 3.251405 object centre (A): 23.76750 20.99200 22.41550 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 94.39265 91.51912 92.48498 assigned negative charge : -311.0742 centred at (gu) : 94.99186 91.46259 92.84440 start vw surface at 0.1300000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 179586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16862 grid for indexing accessible points = 1.400000 m= 99322 mr = 134596 m= 41280 mr = 83015 m= 12137 mr = 34067 m= 2322 mr = 9377 m= 226 mr = 1567 m= 3 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.830000 number of dielectric boundary points 72122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.970000 number of grid points assigned charge 15688 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) : 2.167603 object centre at (A) : 23.76750 20.99200 22.41550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6771186 0.8899381 midg,1,midg; midg,igrid,midg -2.2893062E-02 0.2559026 1,midg,midg; igrid,midg,midg 0.2493403 0.4564997 gauss-seidel spectral radius is 0.9993042 estimated iterations to convergence 299 setup time was (sec) 2.150000 now iterating at: 04:52:51 rms-change max change #iterations 10.51473 328.8872 at 10iterations 6.256348 144.1751 at 20iterations 3.710591 79.20377 at 30iterations 2.199343 47.29620 at 40iterations 1.301024 28.54008 at 50iterations 0.7658317 15.89813 at 60iterations 0.4525084 8.379954 at 70iterations 0.2661129 4.471670 at 80iterations 0.1569237 2.750862 at 90iterations 9.2327744E-02 1.802399 at 100iterations 5.4489098E-02 0.9929428 at 110iterations 3.2198466E-02 0.6257973 at 120iterations 1.9145958E-02 0.3506527 at 130iterations 1.1575279E-02 0.2077551 at 140iterations 7.1528549E-03 0.1214333 at 150iterations 4.5696846E-03 8.2885742E-02 at 160iterations 3.0780360E-03 5.4588318E-02 at 170iterations 2.2077314E-03 3.7006378E-02 at 180iterations finished qdiffx linear iterations at : 04:53:02 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 2.2077314E-03 3.7006378E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 04:53:03 13.151u 0.251s 0:13.84 96.8% 0+0k 0+0io 0pf+0w