Sat Oct 15 11:07:20 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 Sat Oct 15 2011 at 11:07:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3959 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5351372 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): -22.39600 39.28200 ymin,ymax (A): -21.37300 27.74100 zmin,zma (A): -69.55000 -3.025000 x,y,z range (A): 61.67800 49.11400 66.52499 scale (grids/A): 0.5351372 object centre (A): 8.443001 3.184000 -36.28750 number of atom coordinates read : 3959 total number of charged atoms : 3808 net assigned charge : -8.999954 assigned positive charge : 590.9345 centred at (gu) : 91.29224 89.01011 89.00285 assigned negative charge : -599.9363 centred at (gu) : 91.26695 88.91666 88.95448 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7094 nv = 96 ne = 84 npr = 83230 no. pairs analyzed = 83230 no. exposed pairs = 4548 no. arc points = 30630 no. surface atoms = 1544 nbur = 2415 mkacc time = 0.2800000 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 = 1.596000 m= 243 mr = 3953 m= 0 mr = 15 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.5500000 number of dielectric boundary points 3369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3112 ## 392 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 9554 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.2468110E-10 -5.8125151E-11 midg,1,midg; midg,igrid,midg -1.1730565E-09 1.4485012E-10 1,midg,midg; igrid,midg,midg -3.6690936E-10 -2.7956887E-10 gauss-seidel spectral radius is 0.9820676 estimated iterations to convergence 62 setup time was (sec) 0.9100000 now iterating at: 11:07:21 rms-change max change #iterations 7.7652253E-02 12.26097 at 10iterations 5.2688369E-03 0.8568935 at 20iterations 5.8058713E-04 9.2535019E-02 at 30iterations 1.3918553E-04 2.2850990E-02 at 40iterations 3.9067821E-05 6.5889359E-03 at 50iterations finished qdiffx linear iterations at : 11:07:25 total time elapsed so far: 4.960000 # loops : 50 mean,max change (kT/e) : 3.9067821E-05 6.5889359E-03 energy calculations done at 4.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.200000 DelPhi exited at 11:07:26 5.203u 0.460s 0:05.99 94.4% 0+0k 0+0io 5pf+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 15 2011 at 11:07:26 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3959 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: 1.605412 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): -22.39600 39.28200 ymin,ymax (A): -21.37300 27.74100 zmin,zma (A): -69.55000 -3.025000 x,y,z range (A): 61.67800 49.11400 66.52499 scale (grids/A): 1.605412 object centre (A): 8.443001 3.184000 -36.28750 number of atom coordinates read : 3959 total number of charged atoms : 3808 net assigned charge : -8.999954 assigned positive charge : 590.9345 centred at (gu) : 93.87566 87.02921 87.00736 assigned negative charge : -599.9363 centred at (gu) : 93.80034 86.74934 86.86305 start vw surface at 0.1900000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 81027 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30630 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 24061 mr = 58187 m= 2374 mr = 16644 m= 46 mr = 1249 m= 0 mr = 4 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 2368 time to turn everything in is 0.8100000 number of dielectric boundary points 31424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 385 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 29049 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) : 0.5351372 object centre at (A) : 8.443001 3.184000 -36.28750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4014519E-02 -1.5045422E-02 midg,1,midg; midg,igrid,midg -1.5486863E-02 -7.6844823E-05 1,midg,midg; igrid,midg,midg -1.0401498E-03 -4.6809362E-03 gauss-seidel spectral radius is 0.9982061 estimated iterations to convergence 188 setup time was (sec) 1.240000 now iterating at: 11:07:27 rms-change max change #iterations 3.747118 176.1885 at 10iterations 1.568774 60.29948 at 20iterations 0.6569039 21.08938 at 30iterations 0.2765498 8.778999 at 40iterations 0.1159623 3.540094 at 50iterations 4.8721999E-02 1.621330 at 60iterations 2.0584626E-02 0.6559353 at 70iterations 8.6548030E-03 0.2622531 at 80iterations 3.6730263E-03 0.1466637 at 90iterations 1.5652510E-03 4.9012184E-02 at 100iterations 6.7886809E-04 2.3155212E-02 at 110iterations 3.0623420E-04 1.0612488E-02 at 120iterations finished qdiffx linear iterations at : 11:07:38 total time elapsed so far: 11.73000 # loops : 120 mean,max change (kT/e) : 3.0623420E-04 1.0612488E-02 energy calculations done at 11.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.95000 DelPhi exited at 11:07:39 11.955u 0.488s 0:12.91 96.2% 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 15 2011 at 11:07:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3959 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: 2.408118 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): -22.39600 39.28200 ymin,ymax (A): -21.37300 27.74100 zmin,zma (A): -69.55000 -3.025000 x,y,z range (A): 61.67800 49.11400 66.52499 scale (grids/A): 2.408118 object centre (A): 8.443001 3.184000 -36.28750 number of atom coordinates read : 3959 total number of charged atoms : 3808 net assigned charge : -8.999954 assigned positive charge : 590.9345 centred at (gu) : 95.81316 85.54341 85.51080 assigned negative charge : -599.9363 centred at (gu) : 95.70054 85.12392 85.29442 start vw surface at 0.2000000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 189168 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30630 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 86251 mr = 142344 m= 23096 mr = 69412 m= 3775 mr = 17301 m= 226 mr = 2568 m= 1 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 8413 time to turn everything in is 2.020000 number of dielectric boundary points 70806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 2.180000 number of grid points assigned charge 30423 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) : 1.605412 object centre at (A) : 8.443001 3.184000 -36.28750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9409904 -0.3666281 midg,1,midg; midg,igrid,midg -0.2246615 -1.3930014E-02 1,midg,midg; igrid,midg,midg 4.8341040E-02 6.8967417E-03 gauss-seidel spectral radius is 0.9991571 estimated iterations to convergence 272 setup time was (sec) 2.410000 now iterating at: 11:07:42 rms-change max change #iterations 9.720052 301.3442 at 10iterations 5.472733 120.5313 at 20iterations 3.057438 71.39326 at 30iterations 1.711150 35.41844 at 40iterations 0.9528425 17.80101 at 50iterations 0.5295358 10.40164 at 60iterations 0.2948732 5.663147 at 70iterations 0.1633731 2.976990 at 80iterations 9.0708002E-02 1.640085 at 90iterations 5.0222922E-02 0.9134483 at 100iterations 2.7769212E-02 0.5314102 at 110iterations 1.5408200E-02 0.2959399 at 120iterations 8.5599935E-03 0.1646419 at 130iterations 4.7403444E-03 9.5643044E-02 at 140iterations 2.6303355E-03 4.8763275E-02 at 150iterations 1.4616839E-03 2.7820021E-02 at 160iterations 8.1696094E-04 1.5083313E-02 at 170iterations 4.5781175E-04 8.3990097E-03 at 180iterations finished qdiffx linear iterations at : 11:07:59 total time elapsed so far: 19.87000 # loops : 180 mean,max change (kT/e) : 4.5781175E-04 8.3990097E-03 energy calculations done at 19.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.09000 DelPhi exited at 11:08:00 20.095u 0.524s 0:20.93 98.4% 0+0k 0+0io 0pf+0w