Sun Oct 9 23:48:52 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 23:48:52 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 = 3139 !!! 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: 0.5948601 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): -29.19000 30.65600 ymin,ymax (A): 7.651000 61.92000 zmin,zma (A): 24.96700 77.31400 x,y,z range (A): 59.84600 54.26900 52.34700 scale (grids/A): 0.5948601 object centre (A): 0.7329998 34.78550 51.14050 number of atom coordinates read : 3139 total number of charged atoms : 2992 net assigned charge : 2.5008291E-02 assigned positive charge : 473.2529 centred at (gu) : 89.76909 89.17744 88.91286 assigned negative charge : -473.2292 centred at (gu) : 89.78684 89.17498 89.04054 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7421 nv = 96 ne = 84 npr = 62466 no. pairs analyzed = 62466 no. exposed pairs = 4126 no. arc points = 29372 no. surface atoms = 1367 nbur = 1772 mkacc time = 9.9999994E-02 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= 368 mr = 3881 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.2300000 number of dielectric boundary points 3881 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2939 ## 307 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9342 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0816565E-09 -3.8495584E-09 midg,1,midg; midg,igrid,midg -1.7078845E-10 3.7385362E-11 1,midg,midg; igrid,midg,midg 6.5715644E-10 -6.8329925E-10 gauss-seidel spectral radius is 0.9854277 estimated iterations to convergence 68 setup time was (sec) 0.4200000 now iterating at: 23:48:52 rms-change max change #iterations 0.1152773 18.64864 at 10iterations 9.5815854E-03 1.353544 at 20iterations 7.9272862E-04 0.1154776 at 30iterations 6.6476045E-05 1.0062695E-02 at 40iterations 6.6618704E-06 9.9849701E-04 at 50iterations finished qdiffx linear iterations at : 23:48:55 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 6.6618704E-06 9.9849701E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 23:48:56 3.446u 0.164s 0:03.87 93.0% 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 23:48:56 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 = 3139 !!! 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: 1.784580 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): -29.19000 30.65600 ymin,ymax (A): 7.651000 61.92000 zmin,zma (A): 24.96700 77.31400 x,y,z range (A): 59.84600 54.26900 52.34700 scale (grids/A): 1.784580 object centre (A): 0.7329998 34.78550 51.14050 number of atom coordinates read : 3139 total number of charged atoms : 2992 net assigned charge : 2.5008291E-02 assigned positive charge : 473.2529 centred at (gu) : 89.30682 87.53128 86.73787 assigned negative charge : -473.2292 centred at (gu) : 89.36014 87.52452 87.12133 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81109 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29372 grid for indexing accessible points = 1.400000 m= 25985 mr = 54743 m= 3241 mr = 17998 m= 125 mr = 1786 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1520 time to turn everything in is 0.4000000 number of dielectric boundary points 35909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 271 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 23354 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) : 0.5948601 object centre at (A) : 0.7329998 34.78550 51.14050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1725178E-03 -5.9209922E-03 midg,1,midg; midg,igrid,midg 8.0701634E-03 5.7926551E-03 1,midg,midg; igrid,midg,midg 1.9496415E-02 8.2567876E-04 gauss-seidel spectral radius is 0.9985177 estimated iterations to convergence 206 setup time was (sec) 0.6300000 now iterating at: 23:48:57 rms-change max change #iterations 4.170914 170.4848 at 10iterations 1.879987 61.30154 at 20iterations 0.8563312 27.95445 at 30iterations 0.3867802 13.12560 at 40iterations 0.1748887 5.554501 at 50iterations 7.9279251E-02 2.737316 at 60iterations 3.5936587E-02 1.254854 at 70iterations 1.6281368E-02 0.5008087 at 80iterations 7.3786783E-03 0.2412146 at 90iterations 3.3491682E-03 0.1068821 at 100iterations 1.5199017E-03 4.5716763E-02 at 110iterations 6.9110072E-04 2.0519257E-02 at 120iterations finished qdiffx linear iterations at : 23:49:04 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 6.9110072E-04 2.0519257E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.910000 DelPhi exited at 23:49:04 7.913u 0.182s 0:08.35 96.8% 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 23:49:04 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 = 3139 !!! 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: 2.676871 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): -29.19000 30.65600 ymin,ymax (A): 7.651000 61.92000 zmin,zma (A): 24.96700 77.31400 x,y,z range (A): 59.84600 54.26900 52.34700 scale (grids/A): 2.676871 object centre (A): 0.7329998 34.78550 51.14050 number of atom coordinates read : 3139 total number of charged atoms : 2992 net assigned charge : 2.5008291E-02 assigned positive charge : 473.2529 centred at (gu) : 88.96005 86.29671 85.10655 assigned negative charge : -473.2292 centred at (gu) : 89.04012 86.28671 85.68201 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 188282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29372 grid for indexing accessible points = 1.400000 m= 88365 mr = 134018 m= 27334 mr = 70014 m= 5306 mr = 20773 m= 555 mr = 3758 m= 19 mr = 327 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 5121 time to turn everything in is 0.9800000 number of dielectric boundary points 80971 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.070000 number of grid points assigned charge 23924 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) : 1.784580 object centre at (A) : 0.7329998 34.78550 51.14050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1336840 -4.1998597E-03 midg,1,midg; midg,igrid,midg 5.7502463E-02 0.1131349 1,midg,midg; igrid,midg,midg 0.3135875 1.3708301E-02 gauss-seidel spectral radius is 0.9992523 estimated iterations to convergence 289 setup time was (sec) 1.210000 now iterating at: 23:49:06 rms-change max change #iterations 10.33621 278.3621 at 10iterations 6.121958 145.4433 at 20iterations 3.598958 88.44907 at 30iterations 2.103014 45.68988 at 40iterations 1.225892 25.89799 at 50iterations 0.7097948 15.54469 at 60iterations 0.4111426 7.566619 at 70iterations 0.2373380 4.721043 at 80iterations 0.1371470 2.754319 at 90iterations 7.8903459E-02 1.448181 at 100iterations 4.5549169E-02 0.8162222 at 110iterations 2.6243445E-02 0.4735441 at 120iterations 1.5019176E-02 0.2695973 at 130iterations 8.6384322E-03 0.1511459 at 140iterations 4.9598971E-03 9.1609001E-02 at 150iterations 2.8489835E-03 6.0902596E-02 at 160iterations 1.6341172E-03 3.0123711E-02 at 170iterations 9.3966647E-04 1.7518997E-02 at 180iterations finished qdiffx linear iterations at : 23:49:17 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 9.3966647E-04 1.7518997E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.85000 DelPhi exited at 23:49:18 12.853u 0.217s 0:13.33 97.9% 0+0k 0+0io 0pf+0w