Sat Oct 8 11:38:32 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 Sat Oct 8 2011 at 11:38:32 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 = 3130 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: 0.5661848 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): 5.916000 67.18200 ymin,ymax (A): -8.260000 38.79700 zmin,zma (A): -24.46600 38.41100 x,y,z range (A): 61.26600 47.05700 62.87700 scale (grids/A): 0.5661848 object centre (A): 36.54900 15.26850 6.972502 number of atom coordinates read : 3130 total number of charged atoms : 2983 net assigned charge : -9.999969 assigned positive charge : 461.2976 centred at (gu) : 87.95848 90.44340 91.82118 assigned negative charge : -471.2986 centred at (gu) : 87.86172 90.52383 91.91836 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6561 nv = 96 ne = 84 npr = 64270 no. pairs analyzed = 64270 no. exposed pairs = 4018 no. arc points = 27108 no. surface atoms = 1372 nbur = 1758 mkacc time = 0.1100000 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 = 1.512000 m= 305 mr = 3468 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2676 ## 269 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8464 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7395742E-11 -4.1467447E-09 midg,1,midg; midg,igrid,midg -9.9958382E-11 -2.6986453E-09 1,midg,midg; igrid,midg,midg -4.3651203E-09 5.8323041E-11 gauss-seidel spectral radius is 0.9839156 estimated iterations to convergence 65 setup time was (sec) 0.4400000 now iterating at: 11:38:32 rms-change max change #iterations 9.0706214E-02 14.94844 at 10iterations 7.7217114E-03 1.190771 at 20iterations 2.2194546E-03 0.4039707 at 30iterations 1.0902660E-03 0.1995983 at 40iterations 5.4718979E-04 9.9571228E-02 at 50iterations finished qdiffx linear iterations at : 11:38:36 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 5.4718979E-04 9.9571228E-02 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 11:38:36 3.909u 0.243s 0:04.69 88.2% 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 Sat Oct 8 2011 at 11:38:36 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 = 3130 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: 1.698554 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): 5.916000 67.18200 ymin,ymax (A): -8.260000 38.79700 zmin,zma (A): -24.46600 38.41100 x,y,z range (A): 61.26600 47.05700 62.87700 scale (grids/A): 1.698554 object centre (A): 36.54900 15.26850 6.972502 number of atom coordinates read : 3130 total number of charged atoms : 2983 net assigned charge : -9.999969 assigned positive charge : 461.2976 centred at (gu) : 83.87453 91.32896 95.46312 assigned negative charge : -471.2986 centred at (gu) : 83.58468 91.57088 95.75440 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 72423 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27108 grid for indexing accessible points = 1.400000 m= 23575 mr = 50025 m= 2899 mr = 16394 m= 96 mr = 1570 m= 3 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 574 time to turn everything in is 0.3800000 number of dielectric boundary points 30998 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 246 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 23091 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) : 0.5661848 object centre at (A) : 36.54900 15.26850 6.972502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1509901E-03 -2.7287859E-02 midg,1,midg; midg,igrid,midg -8.9389356E-03 -1.4405873E-02 1,midg,midg; igrid,midg,midg -1.8631067E-02 -7.0680245E-03 gauss-seidel spectral radius is 0.9983331 estimated iterations to convergence 194 setup time was (sec) 0.6300000 now iterating at: 11:38:37 rms-change max change #iterations 3.712284 139.5199 at 10iterations 1.603647 59.34526 at 20iterations 0.6940143 27.16528 at 30iterations 0.3017014 10.44613 at 40iterations 0.1305539 4.449263 at 50iterations 5.6979440E-02 1.894555 at 60iterations 2.5282089E-02 0.8303626 at 70iterations 1.1599806E-02 0.4496613 at 80iterations 5.8710594E-03 0.2179470 at 90iterations 3.4900487E-03 0.1371613 at 100iterations 2.4126903E-03 9.7919464E-02 at 110iterations 1.8090889E-03 6.7276001E-02 at 120iterations finished qdiffx linear iterations at : 11:38:45 total time elapsed so far: 8.780000 # loops : 120 mean,max change (kT/e) : 1.8090889E-03 6.7276001E-02 energy calculations done at 8.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.910000 DelPhi exited at 11:38:46 8.913u 0.264s 0:09.49 96.6% 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 Sat Oct 8 2011 at 11:38:46 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 = 3130 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: 2.547831 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): 5.916000 67.18200 ymin,ymax (A): -8.260000 38.79700 zmin,zma (A): -24.46600 38.41100 x,y,z range (A): 61.26600 47.05700 62.87700 scale (grids/A): 2.547831 object centre (A): 36.54900 15.26850 6.972502 number of atom coordinates read : 3130 total number of charged atoms : 2983 net assigned charge : -9.999969 assigned positive charge : 461.2976 centred at (gu) : 80.81165 91.99340 98.19440 assigned negative charge : -471.2986 centred at (gu) : 80.37670 92.35616 98.63158 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 168352 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27108 grid for indexing accessible points = 1.400000 m= 79906 mr = 122221 m= 24805 mr = 63862 m= 4705 mr = 18749 m= 404 mr = 3232 m= 8 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 2103 time to turn everything in is 0.9400000 number of dielectric boundary points 69922 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 23846 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) : 1.698554 object centre at (A) : 36.54900 15.26850 6.972502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1139046 -0.2214268 midg,1,midg; midg,igrid,midg -0.1755629 -0.1657876 1,midg,midg; igrid,midg,midg -0.4187140 -9.0065345E-02 gauss-seidel spectral radius is 0.9991848 estimated iterations to convergence 277 setup time was (sec) 1.240000 now iterating at: 11:38:47 rms-change max change #iterations 9.497157 327.8967 at 10iterations 5.447842 142.5432 at 20iterations 3.117157 79.08212 at 30iterations 1.777011 40.07830 at 40iterations 1.004176 21.71797 at 50iterations 0.5671185 11.43616 at 60iterations 0.3198173 6.129372 at 70iterations 0.1801867 4.022114 at 80iterations 0.1011884 1.932678 at 90iterations 5.6938853E-02 1.218519 at 100iterations 3.2071799E-02 0.6337948 at 110iterations 1.8088982E-02 0.3690453 at 120iterations 1.0330983E-02 0.1942549 at 130iterations 6.0105617E-03 0.1220894 at 140iterations 3.6384116E-03 7.3890686E-02 at 150iterations 2.3654934E-03 5.2989960E-02 at 160iterations 1.6780465E-03 3.7174225E-02 at 170iterations 1.2927457E-03 2.8339386E-02 at 180iterations finished qdiffx linear iterations at : 11:39:01 total time elapsed so far: 15.10000 # loops : 180 mean,max change (kT/e) : 1.2927457E-03 2.8339386E-02 energy calculations done at 15.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.24000 DelPhi exited at 11:39:02 15.241u 0.291s 0:16.31 95.2% 0+0k 0+0io 0pf+0w