Sun Oct 9 23:50:09 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 23:50:09 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3150 !!! WARNING: SEP 138 has a net charge of -0.4750 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: 0.5875654 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): -30.06900 30.52000 ymin,ymax (A): 7.915000 62.06600 zmin,zma (A): 24.87000 77.28800 x,y,z range (A): 60.58900 54.15100 52.41800 scale (grids/A): 0.5875654 object centre (A): 0.2255001 34.99050 51.07900 number of atom coordinates read : 3150 total number of charged atoms : 3003 net assigned charge : 2.5008768E-02 assigned positive charge : 475.5009 centred at (gu) : 90.03582 88.98345 89.01389 assigned negative charge : -475.4772 centred at (gu) : 90.06300 89.00938 89.12520 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7238 nv = 96 ne = 84 npr = 62504 no. pairs analyzed = 62504 no. exposed pairs = 4072 no. arc points = 29038 no. surface atoms = 1359 nbur = 1791 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 = 1.456000 m= 322 mr = 3808 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.2300000 number of dielectric boundary points 3740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2890 ## 315 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9158 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1344284E-09 -2.7252853E-09 midg,1,midg; midg,igrid,midg 9.4401753E-10 -6.4614752E-10 1,midg,midg; igrid,midg,midg 7.7300433E-10 -8.6543855E-10 gauss-seidel spectral radius is 0.9850666 estimated iterations to convergence 67 setup time was (sec) 0.4200000 now iterating at: 23:50:10 rms-change max change #iterations 0.1098427 18.36485 at 10iterations 8.9049274E-03 1.167435 at 20iterations 7.2030898E-04 9.6345901E-02 at 30iterations 5.8592283E-05 9.5863342E-03 at 40iterations 4.7948852E-06 7.1716309E-04 at 50iterations finished qdiffx linear iterations at : 23:50:13 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 4.7948852E-06 7.1716309E-04 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 23:50:13 3.459u 0.165s 0:03.89 92.8% 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 23:50:13 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3150 !!! WARNING: SEP 138 has a net charge of -0.4750 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: 1.762696 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): -30.06900 30.52000 ymin,ymax (A): 7.915000 62.06600 zmin,zma (A): 24.87000 77.28800 x,y,z range (A): 60.58900 54.15100 52.41800 scale (grids/A): 1.762696 object centre (A): 0.2255001 34.99050 51.07900 number of atom coordinates read : 3150 total number of charged atoms : 3003 net assigned charge : 2.5008768E-02 assigned positive charge : 475.5009 centred at (gu) : 90.10658 86.94958 87.04090 assigned negative charge : -475.4772 centred at (gu) : 90.18878 87.02780 87.37546 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29038 grid for indexing accessible points = 1.400000 m= 25440 mr = 54092 m= 3122 mr = 17709 m= 112 mr = 1667 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2437 time to turn everything in is 0.3800000 number of dielectric boundary points 34779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 270 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 23361 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) : 0.5875654 object centre at (A) : 0.2255001 34.99050 51.07900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6672587E-03 -3.0470490E-03 midg,1,midg; midg,igrid,midg 7.4848300E-03 7.8228619E-03 1,midg,midg; igrid,midg,midg 1.3155464E-02 -5.6178393E-03 gauss-seidel spectral radius is 0.9984802 estimated iterations to convergence 203 setup time was (sec) 0.6000000 now iterating at: 23:50:14 rms-change max change #iterations 4.077944 175.4269 at 10iterations 1.829872 60.77143 at 20iterations 0.8149293 29.53256 at 30iterations 0.3662037 12.34075 at 40iterations 0.1643197 5.431472 at 50iterations 7.3838294E-02 2.359208 at 60iterations 3.3136312E-02 1.042749 at 70iterations 1.4847470E-02 0.4666328 at 80iterations 6.6702175E-03 0.2154965 at 90iterations 2.9897809E-03 9.8678112E-02 at 100iterations 1.3448446E-03 4.4507980E-02 at 110iterations 6.0415460E-04 2.0645142E-02 at 120iterations finished qdiffx linear iterations at : 23:50:21 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 6.0415460E-04 2.0645142E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 23:50:22 7.888u 0.187s 0:08.35 96.5% 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 Sun Oct 9 2011 at 23:50:22 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3150 !!! WARNING: SEP 138 has a net charge of -0.4750 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: 2.644044 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): -30.06900 30.52000 ymin,ymax (A): 7.915000 62.06600 zmin,zma (A): 24.87000 77.28800 x,y,z range (A): 60.58900 54.15100 52.41800 scale (grids/A): 2.644044 object centre (A): 0.2255001 34.99050 51.07900 number of atom coordinates read : 3150 total number of charged atoms : 3003 net assigned charge : 2.5008768E-02 assigned positive charge : 475.5009 centred at (gu) : 90.15968 85.42409 85.56106 assigned negative charge : -475.4772 centred at (gu) : 90.28305 85.54154 86.06298 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 184565 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29038 grid for indexing accessible points = 1.400000 m= 86208 mr = 131823 m= 26555 mr = 68597 m= 5104 mr = 20290 m= 421 mr = 3515 m= 6 mr = 206 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 8309 time to turn everything in is 0.9600000 number of dielectric boundary points 78428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 24012 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) : 1.762696 object centre at (A) : 0.2255001 34.99050 51.07900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1374369 9.0578357E-03 midg,1,midg; midg,igrid,midg 6.2502675E-02 0.1605185 1,midg,midg; igrid,midg,midg 0.1430974 -8.3252721E-02 gauss-seidel spectral radius is 0.9992394 estimated iterations to convergence 286 setup time was (sec) 1.210000 now iterating at: 23:50:23 rms-change max change #iterations 10.16259 305.5892 at 10iterations 5.965389 166.7571 at 20iterations 3.477234 78.70106 at 30iterations 2.017252 39.97398 at 40iterations 1.161707 24.09270 at 50iterations 0.6714399 13.78465 at 60iterations 0.3860323 7.869688 at 70iterations 0.2215942 4.321280 at 80iterations 0.1271241 2.343868 at 90iterations 7.2931908E-02 1.454512 at 100iterations 4.1707907E-02 0.8301735 at 110iterations 2.3858862E-02 0.4848537 at 120iterations 1.3637255E-02 0.2425156 at 130iterations 7.7999346E-03 0.1416435 at 140iterations 4.4417717E-03 8.3729744E-02 at 150iterations 2.5417232E-03 4.6983510E-02 at 160iterations 1.4539715E-03 2.8931856E-02 at 170iterations 8.3156180E-04 1.9576550E-02 at 180iterations finished qdiffx linear iterations at : 23:50:34 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 8.3156180E-04 1.9576550E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.83000 DelPhi exited at 23:50:35 12.833u 0.185s 0:13.29 97.8% 0+0k 0+0io 0pf+0w