Mon Oct 10 21:09:28 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 Mon Oct 10 2011 at 21:09:28 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2542 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: 0.6318555 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): -10.14300 45.36800 ymin,ymax (A): 28.20500 81.35300 zmin,zma (A): -10.60700 45.73500 x,y,z range (A): 55.51100 53.14800 56.34200 scale (grids/A): 0.6318555 object centre (A): 17.61250 54.77900 17.56400 number of atom coordinates read : 2542 total number of charged atoms : 2405 net assigned charge : -0.9999936 assigned positive charge : 375.1190 centred at (gu) : 88.99667 90.73325 89.63548 assigned negative charge : -376.1199 centred at (gu) : 88.96733 90.80506 89.58406 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7044 nv = 96 ne = 84 npr = 49965 no. pairs analyzed = 49965 no. exposed pairs = 3549 no. arc points = 25632 no. surface atoms = 1175 nbur = 1367 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 400 mr = 3451 m= 7 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.3000000 number of dielectric boundary points 3932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2542 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8327 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1781611E-09 3.2882816E-09 midg,1,midg; midg,igrid,midg 4.5726938E-09 -8.8934424E-09 1,midg,midg; igrid,midg,midg -4.6015658E-09 1.2691018E-09 gauss-seidel spectral radius is 0.9870382 estimated iterations to convergence 72 setup time was (sec) 0.5100000 now iterating at: 21:09:28 rms-change max change #iterations 0.1319117 20.66542 at 10iterations 1.2866136E-02 2.134979 at 20iterations 1.2558477E-03 0.1996002 at 30iterations 1.2506488E-04 1.8156052E-02 at 40iterations 1.3498674E-05 2.0751953E-03 at 50iterations finished qdiffx linear iterations at : 21:09:31 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 1.3498674E-05 2.0751953E-03 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 21:09:32 3.175u 0.173s 0:04.09 81.6% 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 Mon Oct 10 2011 at 21:09:32 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2542 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: 1.895566 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): -10.14300 45.36800 ymin,ymax (A): 28.20500 81.35300 zmin,zma (A): -10.60700 45.73500 x,y,z range (A): 55.51100 53.14800 56.34200 scale (grids/A): 1.895566 object centre (A): 17.61250 54.77900 17.56400 number of atom coordinates read : 2542 total number of charged atoms : 2405 net assigned charge : -0.9999936 assigned positive charge : 375.1190 centred at (gu) : 86.98929 92.19930 88.90598 assigned negative charge : -376.1199 centred at (gu) : 86.90218 92.41525 88.75207 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 75775 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25632 grid for indexing accessible points = 1.400000 m= 26404 mr = 49399 m= 4322 mr = 18404 m= 257 mr = 2561 m= 1 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 1936 time to turn everything in is 0.5300000 number of dielectric boundary points 36306 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 18917 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) : 0.6318555 object centre at (A) : 17.61250 54.77900 17.56400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0521965E-03 -1.1797968E-02 midg,1,midg; midg,igrid,midg 1.8505137E-02 -2.4598839E-02 1,midg,midg; igrid,midg,midg -3.5508007E-03 2.7407538E-03 gauss-seidel spectral radius is 0.9986431 estimated iterations to convergence 215 setup time was (sec) 0.8000000 now iterating at: 21:09:33 rms-change max change #iterations 4.167950 168.9961 at 10iterations 1.946827 73.14859 at 20iterations 0.9107928 28.49892 at 30iterations 0.4265750 13.32590 at 40iterations 0.1997693 6.688221 at 50iterations 9.3518198E-02 2.903915 at 60iterations 4.3780729E-02 1.383055 at 70iterations 2.0523787E-02 0.6847327 at 80iterations 9.6287727E-03 0.2886677 at 90iterations 4.5091072E-03 0.1338367 at 100iterations 2.1156999E-03 7.0230484E-02 at 110iterations 9.8859018E-04 3.7269592E-02 at 120iterations finished qdiffx linear iterations at : 21:09:39 total time elapsed so far: 7.300000 # loops : 120 mean,max change (kT/e) : 9.8859018E-04 3.7269592E-02 energy calculations done at 7.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 21:09:40 7.468u 0.246s 0:08.15 94.4% 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 Mon Oct 10 2011 at 21:09:40 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2542 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: 2.843350 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): -10.14300 45.36800 ymin,ymax (A): 28.20500 81.35300 zmin,zma (A): -10.60700 45.73500 x,y,z range (A): 55.51100 53.14800 56.34200 scale (grids/A): 2.843350 object centre (A): 17.61250 54.77900 17.56400 number of atom coordinates read : 2542 total number of charged atoms : 2405 net assigned charge : -0.9999936 assigned positive charge : 375.1190 centred at (gu) : 85.48392 93.29911 88.35888 assigned negative charge : -376.1199 centred at (gu) : 85.35334 93.62277 88.12820 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 175103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25632 grid for indexing accessible points = 1.400000 m= 84531 mr = 120696 m= 30949 mr = 66585 m= 7736 mr = 23877 m= 1129 mr = 5611 m= 66 mr = 739 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.7699999 no. cavity mid-points inaccessible to solvent = 6455 time to turn everything in is 1.340000 number of dielectric boundary points 81981 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 19240 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) : 1.895566 object centre at (A) : 17.61250 54.77900 17.56400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1018690 -0.1105981 midg,1,midg; midg,igrid,midg 0.2242068 -0.1828664 1,midg,midg; igrid,midg,midg 0.1754866 6.8992050E-03 gauss-seidel spectral radius is 0.9992764 estimated iterations to convergence 293 setup time was (sec) 1.660000 now iterating at: 21:09:42 rms-change max change #iterations 9.969164 343.5782 at 10iterations 5.905066 160.9888 at 20iterations 3.475520 88.17850 at 30iterations 2.037135 53.59040 at 40iterations 1.187652 24.85782 at 50iterations 0.6914719 14.50799 at 60iterations 0.4029393 8.054214 at 70iterations 0.2335450 4.703001 at 80iterations 0.1355319 2.788427 at 90iterations 7.8381203E-02 1.476079 at 100iterations 4.5397826E-02 0.8217940 at 110iterations 2.6265478E-02 0.4905090 at 120iterations 1.5175616E-02 0.3004513 at 130iterations 8.7691210E-03 0.1591015 at 140iterations 5.0720689E-03 9.7428739E-02 at 150iterations 2.9352922E-03 5.6026459E-02 at 160iterations 1.6978468E-03 2.9685974E-02 at 170iterations 9.8064437E-04 1.7393112E-02 at 180iterations finished qdiffx linear iterations at : 21:09:52 total time elapsed so far: 12.03000 # loops : 180 mean,max change (kT/e) : 9.8064437E-04 1.7393112E-02 energy calculations done at 12.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 21:09:53 12.199u 0.213s 0:12.92 95.9% 0+0k 0+0io 0pf+0w