Sat Oct 8 11:43:27 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 Sat Oct 8 2011 at 11:43:27 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4508 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5591330 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): -25.49500 34.95600 ymin,ymax (A): 34.93500 98.60500 zmin,zma (A): 30.03300 87.54500 x,y,z range (A): 60.45100 63.67000 57.51200 scale (grids/A): 0.5591330 object centre (A): 4.730499 66.77000 58.78900 number of atom coordinates read : 4508 total number of charged atoms : 4349 net assigned charge : -0.9999603 assigned positive charge : 681.4046 centred at (gu) : 90.62652 88.16866 89.20100 assigned negative charge : -682.4082 centred at (gu) : 90.51646 88.29811 89.34846 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8600 nv = 96 ne = 84 npr = 96971 no. pairs analyzed = 96971 no. exposed pairs = 4945 no. arc points = 33487 no. surface atoms = 1683 nbur = 2825 mkacc time = 0.2700000 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 = 1.540000 m= 355 mr = 4924 m= 0 mr = 22 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 85 time to turn everything in is 0.5500000 number of dielectric boundary points 4009 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3524 ## 430 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 11696 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.6851930E-09 -2.1733120E-09 midg,1,midg; midg,igrid,midg 3.0277509E-09 -1.4965269E-09 1,midg,midg; igrid,midg,midg -1.7230115E-09 1.8773738E-09 gauss-seidel spectral radius is 0.9835996 estimated iterations to convergence 64 setup time was (sec) 0.8200000 now iterating at: 11:43:28 rms-change max change #iterations 0.1041313 14.73156 at 10iterations 7.5839362E-03 0.9477234 at 20iterations 7.4395008E-04 0.1017532 at 30iterations 1.8673319E-04 2.7084351E-02 at 40iterations 6.7204644E-05 1.0063171E-02 at 50iterations finished qdiffx linear iterations at : 11:43:32 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 6.7204644E-05 1.0063171E-02 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 11:43:32 4.376u 0.269s 0:04.94 93.7% 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 Sat Oct 8 2011 at 11:43:32 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4508 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.677399 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): -25.49500 34.95600 ymin,ymax (A): 34.93500 98.60500 zmin,zma (A): 30.03300 87.54500 x,y,z range (A): 60.45100 63.67000 57.51200 scale (grids/A): 1.677399 object centre (A): 4.730499 66.77000 58.78900 number of atom coordinates read : 4508 total number of charged atoms : 4349 net assigned charge : -0.9999603 assigned positive charge : 681.4046 centred at (gu) : 91.87795 84.50473 87.60167 assigned negative charge : -682.4082 centred at (gu) : 91.54916 84.89407 88.04506 start vw surface at 0.2100000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 97239 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33487 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30694 mr = 70274 m= 3477 mr = 22276 m= 102 mr = 1974 m= 0 mr = 20 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 6893 time to turn everything in is 0.8400000 number of dielectric boundary points 36968 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 380 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 33476 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) : 0.5591330 object centre at (A) : 4.730499 66.77000 58.78900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4582633E-02 -2.6226545E-02 midg,1,midg; midg,igrid,midg 3.0323263E-02 -5.9720632E-03 1,midg,midg; igrid,midg,midg -5.7166750E-03 3.1997435E-02 gauss-seidel spectral radius is 0.9984077 estimated iterations to convergence 199 setup time was (sec) 1.160000 now iterating at: 11:43:34 rms-change max change #iterations 4.497599 161.1449 at 10iterations 1.982512 61.39756 at 20iterations 0.8786968 26.15064 at 30iterations 0.3890182 11.95343 at 40iterations 0.1712877 5.184601 at 50iterations 7.5758874E-02 2.218028 at 60iterations 3.3566963E-02 0.9138041 at 70iterations 1.4792790E-02 0.4184723 at 80iterations 6.5841139E-03 0.1914749 at 90iterations 2.9308049E-03 9.3157291E-02 at 100iterations 1.3254288E-03 3.8174629E-02 at 110iterations 6.1275612E-04 1.7797470E-02 at 120iterations finished qdiffx linear iterations at : 11:43:42 total time elapsed so far: 9.790000 # loops : 120 mean,max change (kT/e) : 6.1275612E-04 1.7797470E-02 energy calculations done at 9.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.960000 DelPhi exited at 11:43:43 9.964u 0.314s 0:10.62 96.7% 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 Sat Oct 8 2011 at 11:43:43 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4508 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.516098 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): -25.49500 34.95600 ymin,ymax (A): 34.93500 98.60500 zmin,zma (A): 30.03300 87.54500 x,y,z range (A): 60.45100 63.67000 57.51200 scale (grids/A): 2.516098 object centre (A): 4.730499 66.77000 58.78900 number of atom coordinates read : 4508 total number of charged atoms : 4349 net assigned charge : -0.9999603 assigned positive charge : 681.4046 centred at (gu) : 92.81663 81.75697 86.40217 assigned negative charge : -682.4082 centred at (gu) : 92.32349 82.34078 87.06747 start vw surface at 0.2100000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 226871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33487 grid for indexing accessible points = 1.400000 m= 106810 mr = 171302 m= 31349 mr = 87407 m= 5776 mr = 24626 m= 479 mr = 4180 m= 10 mr = 256 m= 0 mr = 2 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 22289 time to turn everything in is 2.090000 number of dielectric boundary points 83522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 34771 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) : 1.677399 object centre at (A) : 4.730499 66.77000 58.78900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1895606 -0.3391335 midg,1,midg; midg,igrid,midg 0.4059917 1.0302247E-02 1,midg,midg; igrid,midg,midg -0.2070381 0.3739776 gauss-seidel spectral radius is 0.9992213 estimated iterations to convergence 283 setup time was (sec) 2.450000 now iterating at: 11:43:45 rms-change max change #iterations 11.21593 303.9496 at 10iterations 6.447577 117.5319 at 20iterations 3.690278 63.24277 at 30iterations 2.111292 38.32418 at 40iterations 1.203802 20.94141 at 50iterations 0.6856384 11.51651 at 60iterations 0.3898548 6.516972 at 70iterations 0.2217088 3.993062 at 80iterations 0.1257986 2.094559 at 90iterations 7.1461178E-02 1.168572 at 100iterations 4.0622223E-02 0.7015762 at 110iterations 2.3049699E-02 0.3876028 at 120iterations 1.3099423E-02 0.2251619 at 130iterations 7.4443026E-03 0.1230187 at 140iterations 4.2316988E-03 7.2178721E-02 at 150iterations 2.4234818E-03 4.3122053E-02 at 160iterations 1.3987602E-03 2.6165962E-02 at 170iterations 8.1730942E-04 1.5525818E-02 at 180iterations finished qdiffx linear iterations at : 11:44:00 total time elapsed so far: 17.00000 # loops : 180 mean,max change (kT/e) : 8.1730942E-04 1.5525818E-02 energy calculations done at 17.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.18000 DelPhi exited at 11:44:01 17.186u 0.335s 0:17.82 98.2% 0+0k 0+0io 0pf+0w