Tue Oct 11 03:21:53 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 03:21:53 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1186 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7502317 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): -6.613000 30.35700 ymin,ymax (A): 1.376000 40.07900 zmin,zma (A): -1.344000 46.10800 x,y,z range (A): 36.97000 38.70300 47.45200 scale (grids/A): 0.7502317 object centre (A): 11.87200 20.72750 22.38200 number of atom coordinates read : 1186 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 89.28810 89.18062 88.45755 assigned negative charge : -169.8232 centred at (gu) : 88.98573 89.16531 88.49732 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4579 nv = 96 ne = 84 npr = 23122 no. pairs analyzed = 23122 no. exposed pairs = 1532 no. arc points = 11227 no. surface atoms = 516 nbur = 670 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 285 mr = 2370 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 44 time to turn everything in is 0.1200000 number of dielectric boundary points 2456 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 913 ## 96 charges are in solution ## iepsmp to db, and charging done at 0.1800000 number of grid points assigned charge 4586 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9586230E-07 7.3116880E-08 midg,1,midg; midg,igrid,midg 1.2923832E-07 1.1403144E-07 1,midg,midg; igrid,midg,midg -9.6885643E-08 2.7696115E-07 gauss-seidel spectral radius is 0.9906458 estimated iterations to convergence 84 setup time was (sec) 0.3200000 now iterating at: 03:21:53 rms-change max change #iterations 0.1863225 38.70937 at 10iterations 2.5559863E-02 4.460050 at 20iterations 3.4546889E-03 0.5248337 at 30iterations 4.7455111E-04 7.5289488E-02 at 40iterations 6.2886662E-05 9.5548630E-03 at 50iterations finished qdiffx linear iterations at : 03:21:56 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 6.2886662E-05 9.5548630E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 03:21:57 3.323u 0.155s 0:03.75 92.5% 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 Tue Oct 11 2011 at 03:21:57 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1186 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.250695 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): -6.613000 30.35700 ymin,ymax (A): 1.376000 40.07900 zmin,zma (A): -1.344000 46.10800 x,y,z range (A): 36.97000 38.70300 47.45200 scale (grids/A): 2.250695 object centre (A): 11.87200 20.72750 22.38200 number of atom coordinates read : 1186 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 87.86446 87.54187 85.37276 assigned negative charge : -169.8232 centred at (gu) : 86.95733 87.49611 85.49218 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 47814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11227 grid for indexing accessible points = 1.400000 m= 17784 mr = 31193 m= 3510 mr = 13212 m= 346 mr = 2350 m= 20 mr = 198 m= 0 mr = 2 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 1429 time to turn everything in is 0.2500000 number of dielectric boundary points 22519 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 41 iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8468 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) : 0.7502317 object centre at (A) : 11.87200 20.72750 22.38200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6320120E-02 4.4740466E-03 midg,1,midg; midg,igrid,midg 4.1127816E-02 3.4292649E-02 1,midg,midg; igrid,midg,midg -2.5575578E-02 4.5633368E-02 gauss-seidel spectral radius is 0.9988646 estimated iterations to convergence 235 setup time was (sec) 0.4600000 now iterating at: 03:21:57 rms-change max change #iterations 3.675261 200.6227 at 10iterations 1.830724 79.27985 at 20iterations 0.9170567 38.18261 at 30iterations 0.4574458 20.82853 at 40iterations 0.2287835 9.347626 at 50iterations 0.1143582 4.668353 at 60iterations 5.7018179E-02 2.072164 at 70iterations 2.8505281E-02 0.9539185 at 80iterations 1.4174197E-02 0.5141983 at 90iterations 7.0766797E-03 0.2570419 at 100iterations 3.5389827E-03 0.1308746 at 110iterations 1.7718753E-03 6.2425137E-02 at 120iterations finished qdiffx linear iterations at : 03:22:04 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 1.7718753E-03 6.2425137E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 03:22:05 7.617u 0.209s 0:08.38 93.1% 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 03:22:05 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1186 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.376043 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): -6.613000 30.35700 ymin,ymax (A): 1.376000 40.07900 zmin,zma (A): -1.344000 46.10800 x,y,z range (A): 36.97000 38.70300 47.45200 scale (grids/A): 3.376043 object centre (A): 11.87200 20.72750 22.38200 number of atom coordinates read : 1186 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 86.79675 86.31279 83.05917 assigned negative charge : -169.8232 centred at (gu) : 85.43612 86.24422 83.23835 start vw surface at 5.0000001E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 109875 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11227 grid for indexing accessible points = 1.400000 m= 55047 mr = 75284 m= 22561 mr = 44824 m= 6641 mr = 18466 m= 1344 mr = 5146 m= 210 mr = 996 m= 25 mr = 145 m= 0 mr = 20 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 4683 time to turn everything in is 0.7400000 number of dielectric boundary points 50822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 8488 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) : 2.250695 object centre at (A) : 11.87200 20.72750 22.38200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3230426 6.4989403E-03 midg,1,midg; midg,igrid,midg 0.3623765 0.2882472 1,midg,midg; igrid,midg,midg -0.1966703 0.3330776 gauss-seidel spectral radius is 0.9992979 estimated iterations to convergence 298 setup time was (sec) 0.9700000 now iterating at: 03:22:06 rms-change max change #iterations 7.923356 293.8070 at 10iterations 4.624628 123.9129 at 20iterations 2.686597 60.99426 at 30iterations 1.558638 36.02481 at 40iterations 0.9060231 19.85911 at 50iterations 0.5260212 10.80962 at 60iterations 0.3048925 6.697263 at 70iterations 0.1768806 3.620453 at 80iterations 0.1025702 2.151772 at 90iterations 5.9919428E-02 1.372665 at 100iterations 3.4627058E-02 0.7344666 at 110iterations 2.0159828E-02 0.4796171 at 120iterations 1.1701825E-02 0.2496910 at 130iterations 6.8124435E-03 0.1383452 at 140iterations 3.9501344E-03 7.9841614E-02 at 150iterations 2.3022965E-03 4.5398712E-02 at 160iterations 1.3338025E-03 2.8686523E-02 at 170iterations 7.7781355E-04 1.7138243E-02 at 180iterations finished qdiffx linear iterations at : 03:22:17 total time elapsed so far: 11.79000 # loops : 180 mean,max change (kT/e) : 7.7781355E-04 1.7138243E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 03:22:17 11.928u 0.201s 0:12.43 97.5% 0+0k 0+0io 0pf+0w