Sun Oct 9 13:01:23 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+sph2.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 = amb2.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 13:01:23 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 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: 0.6827248 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): -7.583000 44.56100 ymin,ymax (A): -13.90800 36.91000 zmin,zma (A): 2.575000 44.91100 x,y,z range (A): 52.14400 50.81800 42.33600 scale (grids/A): 0.6827248 object centre (A): 18.48900 11.50100 23.74300 number of atom coordinates read : 2367 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 363.5892 centred at (gu) : 89.93130 91.32357 90.68923 assigned negative charge : -360.0896 centred at (gu) : 89.94700 91.47722 90.73089 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7596 nv = 96 ne = 84 npr = 47260 no. pairs analyzed = 47260 no. exposed pairs = 2935 no. arc points = 20961 no. surface atoms = 993 nbur = 1374 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 455 mr = 4220 m= 3 mr = 78 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 0.2700000 number of dielectric boundary points 3756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2017 ## 205 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8486 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6427985E-08 3.9120511E-09 midg,1,midg; midg,igrid,midg 5.0251042E-08 -4.4088342E-08 1,midg,midg; igrid,midg,midg 2.2314328E-08 1.1767470E-08 gauss-seidel spectral radius is 0.9888570 estimated iterations to convergence 77 setup time was (sec) 0.4900000 now iterating at: 13:01:24 rms-change max change #iterations 0.1875979 27.37188 at 10iterations 2.2130134E-02 3.289816 at 20iterations 3.1853144E-03 0.4629135 at 30iterations 7.7202643E-04 0.1211548 at 40iterations 2.5900453E-04 4.1000366E-02 at 50iterations finished qdiffx linear iterations at : 13:01:26 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 2.5900453E-04 4.1000366E-02 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 13:01:26 3.064u 0.155s 0:03.49 91.9% 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 13:01:27 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.048174 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): -7.583000 44.56100 ymin,ymax (A): -13.90800 36.91000 zmin,zma (A): 2.575000 44.91100 x,y,z range (A): 52.14400 50.81800 42.33600 scale (grids/A): 2.048174 object centre (A): 18.48900 11.50100 23.74300 number of atom coordinates read : 2367 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 363.5892 centred at (gu) : 89.79346 93.97039 92.06713 assigned negative charge : -360.0896 centred at (gu) : 89.84087 94.43164 92.19232 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79773 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20961 grid for indexing accessible points = 1.400000 m= 31528 mr = 55180 m= 5567 mr = 23786 m= 433 mr = 3603 m= 14 mr = 199 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 0.5700000 number of dielectric boundary points 34547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 123 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 17634 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) : 0.6827248 object centre at (A) : 18.48900 11.50100 23.74300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5010988E-02 8.5042836E-03 midg,1,midg; midg,igrid,midg 1.3913164E-02 -3.6629517E-02 1,midg,midg; igrid,midg,midg 5.0207399E-02 -8.4736636E-03 gauss-seidel spectral radius is 0.9987944 estimated iterations to convergence 228 setup time was (sec) 0.8300000 now iterating at: 13:01:27 rms-change max change #iterations 4.726099 227.4431 at 10iterations 2.306074 84.31808 at 20iterations 1.132573 40.24146 at 30iterations 0.5560935 17.16162 at 40iterations 0.2726784 8.862253 at 50iterations 0.1334363 3.909207 at 60iterations 6.5973580E-02 1.902741 at 70iterations 3.2470632E-02 0.9425216 at 80iterations 1.6184002E-02 0.4725685 at 90iterations 8.1005180E-03 0.2499123 at 100iterations 4.1688313E-03 0.1310301 at 110iterations 2.2323432E-03 7.7487946E-02 at 120iterations finished qdiffx linear iterations at : 13:01:33 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 2.2323432E-03 7.7487946E-02 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 13:01:34 6.897u 0.155s 0:07.33 96.0% 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 Sun Oct 9 2011 at 13:01:34 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: 305 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2367 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: 3.072262 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): -7.583000 44.56100 ymin,ymax (A): -13.90800 36.91000 zmin,zma (A): 2.575000 44.91100 x,y,z range (A): 52.14400 50.81800 42.33600 scale (grids/A): 3.072262 object centre (A): 18.48900 11.50100 23.74300 number of atom coordinates read : 2367 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 363.5892 centred at (gu) : 89.69022 95.95564 93.10065 assigned negative charge : -360.0896 centred at (gu) : 89.76132 96.64744 93.28832 start vw surface at 0.1300000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 183822 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20961 grid for indexing accessible points = 1.400000 m= 98266 mr = 133163 m= 39133 mr = 81218 m= 10245 mr = 31973 m= 1848 mr = 7902 m= 171 mr = 1293 m= 5 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.420000 number of dielectric boundary points 77861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 17798 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) : 2.048174 object centre at (A) : 18.48900 11.50100 23.74300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4676685 -1.5540294E-02 midg,1,midg; midg,igrid,midg 0.3290598 -0.4420319 1,midg,midg; igrid,midg,midg 0.4939670 -0.4472739 gauss-seidel spectral radius is 0.9992905 estimated iterations to convergence 296 setup time was (sec) 1.710000 now iterating at: 13:01:36 rms-change max change #iterations 10.71752 400.7089 at 10iterations 6.334538 127.1274 at 20iterations 3.725202 73.62938 at 30iterations 2.197362 43.57214 at 40iterations 1.290478 24.54089 at 50iterations 0.7544614 17.49874 at 60iterations 0.4422813 8.307764 at 70iterations 0.2587244 4.982979 at 80iterations 0.1511949 2.570757 at 90iterations 8.8624328E-02 1.519110 at 100iterations 5.1786289E-02 0.9092119 at 110iterations 3.0486334E-02 0.5390091 at 120iterations 1.8077957E-02 0.3504086 at 130iterations 1.0909164E-02 0.2002792 at 140iterations 6.8052895E-03 0.1446152 at 150iterations 4.4318107E-03 8.8378906E-02 at 160iterations 3.0753247E-03 6.6759109E-02 at 170iterations 2.2746737E-03 4.7828674E-02 at 180iterations finished qdiffx linear iterations at : 13:01:45 total time elapsed so far: 11.06000 # loops : 180 mean,max change (kT/e) : 2.2746737E-03 4.7828674E-02 energy calculations done at 11.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.24000 DelPhi exited at 13:01:46 11.242u 0.166s 0:11.68 97.6% 0+0k 0+0io 0pf+0w