Tue Oct 11 08:33:15 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 08:33:15 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7165285 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): -19.29100 24.93400 ymin,ymax (A): -13.06700 27.90800 zmin,zma (A): -3.469000 46.21500 x,y,z range (A): 44.22500 40.97500 49.68400 scale (grids/A): 0.7165285 object centre (A): 2.821500 7.420500 21.37300 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) : 89.56549 90.08828 90.76884 assigned negative charge : -311.0742 centred at (gu) : 89.43708 90.08958 90.83239 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6823 nv = 96 ne = 84 npr = 44044 no. pairs analyzed = 44044 no. exposed pairs = 2352 no. arc points = 16046 no. surface atoms = 809 nbur = 1280 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 3954 m= 3 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3254 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1509 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7917 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.2149207E-08 3.4276812E-08 midg,1,midg; midg,igrid,midg 6.8206091E-08 6.8884042E-08 1,midg,midg; igrid,midg,midg -1.1002538E-08 1.3331503E-07 gauss-seidel spectral radius is 0.9898369 estimated iterations to convergence 81 setup time was (sec) 0.5900000 now iterating at: 08:33:16 rms-change max change #iterations 0.2141173 29.08973 at 10iterations 2.6968025E-02 3.756965 at 20iterations 3.4593714E-03 0.5328155 at 30iterations 4.4866503E-04 6.7544937E-02 at 40iterations 6.0562743E-05 8.9263916E-03 at 50iterations finished qdiffx linear iterations at : 08:33:19 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 6.0562743E-05 8.9263916E-03 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.190000 DelPhi exited at 08:33:20 4.193u 0.281s 0:04.96 90.1% 0+0k 0+0io 6pf+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 08:33:20 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: 2.149585 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): -19.29100 24.93400 ymin,ymax (A): -13.06700 27.90800 zmin,zma (A): -3.469000 46.21500 x,y,z range (A): 44.22500 40.97500 49.68400 scale (grids/A): 2.149585 object centre (A): 2.821500 7.420500 21.37300 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) : 88.69630 90.26477 92.30642 assigned negative charge : -311.0742 centred at (gu) : 88.31132 90.26883 92.49732 start vw surface at 0.1200000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 73580 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16046 grid for indexing accessible points = 1.400000 m= 27038 mr = 52738 m= 4878 mr = 20146 m= 401 mr = 3061 m= 8 mr = 181 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 29779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 71 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15593 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) : 0.7165285 object centre at (A) : 2.821500 7.420500 21.37300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1961577E-02 7.0760705E-02 midg,1,midg; midg,igrid,midg 2.7118890E-02 1.1201884E-02 1,midg,midg; igrid,midg,midg -3.7651558E-03 3.3981569E-02 gauss-seidel spectral radius is 0.9988475 estimated iterations to convergence 233 setup time was (sec) 0.9600000 now iterating at: 08:33:21 rms-change max change #iterations 4.713504 178.4902 at 10iterations 2.334934 69.59165 at 20iterations 1.162244 36.59256 at 30iterations 0.5815754 16.81406 at 40iterations 0.2890068 8.846432 at 50iterations 0.1446314 4.151776 at 60iterations 7.2334990E-02 2.289362 at 70iterations 3.6038138E-02 1.111553 at 80iterations 1.7974772E-02 0.5176239 at 90iterations 8.9916969E-03 0.2753320 at 100iterations 4.4830362E-03 0.1379328 at 110iterations 2.2451137E-03 7.4169159E-02 at 120iterations finished qdiffx linear iterations at : 08:33:30 total time elapsed so far: 9.610000 # loops : 120 mean,max change (kT/e) : 2.2451137E-03 7.4169159E-02 energy calculations done at 9.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.790000 DelPhi exited at 08:33:31 9.795u 0.349s 0:10.61 95.4% 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 Tue Oct 11 2011 at 08:33:31 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 = 2089 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: 3.224378 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): -19.29100 24.93400 ymin,ymax (A): -13.06700 27.90800 zmin,zma (A): -3.469000 46.21500 x,y,z range (A): 44.22500 40.97500 49.68400 scale (grids/A): 3.224378 object centre (A): 2.821500 7.420500 21.37300 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) : 88.04458 90.39717 93.45955 assigned negative charge : -311.0742 centred at (gu) : 87.46698 90.40333 93.74590 start vw surface at 0.1500000 fill in re-entrant regions at 1.030000 boundary points on vw surface= 170249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16046 grid for indexing accessible points = 1.400000 m= 87182 mr = 127291 m= 32897 mr = 71985 m= 8998 mr = 26631 m= 1641 mr = 6749 m= 169 mr = 1116 m= 3 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.170000 number of dielectric boundary points 67276 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.320000 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) : 2.149585 object centre at (A) : 2.821500 7.420500 21.37300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2573273 0.7194392 midg,1,midg; midg,igrid,midg 0.2160147 5.3646155E-02 1,midg,midg; igrid,midg,midg 2.9820200E-02 0.3004678 gauss-seidel spectral radius is 0.9992939 estimated iterations to convergence 297 setup time was (sec) 2.500000 now iterating at: 08:33:33 rms-change max change #iterations 10.41152 333.1467 at 10iterations 6.142240 120.5341 at 20iterations 3.605104 66.33155 at 30iterations 2.120815 38.27110 at 40iterations 1.241625 23.86699 at 50iterations 0.7289991 16.98052 at 60iterations 0.4256184 7.693940 at 70iterations 0.2489351 5.312893 at 80iterations 0.1458262 2.441280 at 90iterations 8.5347913E-02 1.526941 at 100iterations 4.9834222E-02 0.8208084 at 110iterations 2.9159907E-02 0.5049868 at 120iterations 1.7089596E-02 0.3026543 at 130iterations 1.0027580E-02 0.1850281 at 140iterations 5.9463992E-03 0.1156540 at 150iterations 3.5431220E-03 6.1151505E-02 at 160iterations 2.1511265E-03 3.7210226E-02 at 170iterations 1.3414721E-03 2.3914337E-02 at 180iterations finished qdiffx linear iterations at : 08:33:48 total time elapsed so far: 16.77000 # loops : 180 mean,max change (kT/e) : 1.3414721E-03 2.3914337E-02 energy calculations done at 16.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.95000 DelPhi exited at 08:33:48 16.949u 0.352s 0:17.69 97.7% 0+0k 0+0io 0pf+0w