Sun Oct 9 09:40:02 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 Sun Oct 9 2011 at 09:40:02 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 = 3142 !!! WARNING: TYR 304 has a net charge of -0.2720 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: 0.4942659 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): -38.37900 16.57500 ymin,ymax (A): 3.324000 52.65700 zmin,zma (A): -3.125000 68.90100 x,y,z range (A): 54.95400 49.33300 72.02600 scale (grids/A): 0.4942659 object centre (A): -10.90200 27.99050 32.88800 number of atom coordinates read : 3142 total number of charged atoms : 2991 net assigned charge : 3.228023 assigned positive charge : 463.4311 centred at (gu) : 91.31303 89.82874 89.10979 assigned negative charge : -460.2041 centred at (gu) : 91.34828 89.84881 89.06342 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5022 nv = 96 ne = 84 npr = 60406 no. pairs analyzed = 60406 no. exposed pairs = 4459 no. arc points = 31703 no. surface atoms = 1477 nbur = 1665 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 = 1.708000 m= 192 mr = 2322 m= 0 mr = 6 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2886 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2971 ## 454 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6700 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0129136E-11 4.6888219E-11 midg,1,midg; midg,igrid,midg 4.0341903E-11 5.7617019E-12 1,midg,midg; igrid,midg,midg 3.5651648E-11 -9.6987921E-12 gauss-seidel spectral radius is 0.9789737 estimated iterations to convergence 57 setup time was (sec) 0.4000000 now iterating at: 09:40:02 rms-change max change #iterations 4.4398133E-02 10.32647 at 10iterations 2.2191510E-03 0.5290165 at 20iterations 1.1658963E-04 1.9943237E-02 at 30iterations 8.0127957E-06 1.7814636E-03 at 40iterations 1.2165848E-06 3.0994415E-04 at 50iterations finished qdiffx linear iterations at : 09:40:05 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.2165848E-06 3.0994415E-04 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 09:40:06 3.487u 0.190s 0:03.99 91.9% 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 09:40:06 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 = 3142 !!! WARNING: TYR 304 has a net charge of -0.2720 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: 1.482798 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): -38.37900 16.57500 ymin,ymax (A): 3.324000 52.65700 zmin,zma (A): -3.125000 68.90100 x,y,z range (A): 54.95400 49.33300 72.02600 scale (grids/A): 1.482798 object centre (A): -10.90200 27.99050 32.88800 number of atom coordinates read : 3142 total number of charged atoms : 2991 net assigned charge : 3.228023 assigned positive charge : 463.4311 centred at (gu) : 93.93805 89.48533 87.32873 assigned negative charge : -460.2041 centred at (gu) : 94.04440 89.54596 87.19028 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 55818 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31703 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 15963 mr = 35316 m= 1353 mr = 10218 m= 26 mr = 487 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 228 time to turn everything in is 0.2800000 number of dielectric boundary points 27139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 458 ## 15 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 22272 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) : 0.4942659 object centre at (A) : -10.90200 27.99050 32.88800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4610074E-03 -1.1027820E-02 midg,1,midg; midg,igrid,midg 5.2303527E-03 3.0948743E-04 1,midg,midg; igrid,midg,midg 3.0015027E-03 -1.8666062E-03 gauss-seidel spectral radius is 0.9978110 estimated iterations to convergence 170 setup time was (sec) 0.4800000 now iterating at: 09:40:06 rms-change max change #iterations 2.697094 134.7947 at 10iterations 1.022136 45.33182 at 20iterations 0.3924468 18.26392 at 30iterations 0.1492338 6.408659 at 40iterations 5.7192110E-02 2.346652 at 50iterations 2.1822251E-02 0.8359756 at 60iterations 8.3293170E-03 0.3183403 at 70iterations 3.2065061E-03 0.1421623 at 80iterations 1.2316667E-03 5.1792145E-02 at 90iterations 4.7784374E-04 2.1705627E-02 at 100iterations 1.8786172E-04 8.4609985E-03 at 110iterations 7.7445970E-05 3.3111572E-03 at 120iterations finished qdiffx linear iterations at : 09:40:13 total time elapsed so far: 7.550000 # loops : 120 mean,max change (kT/e) : 7.7445970E-05 3.3111572E-03 energy calculations done at 7.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.690000 DelPhi exited at 09:40:14 7.692u 0.224s 0:08.25 95.8% 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 09:40:14 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 = 3142 !!! WARNING: TYR 304 has a net charge of -0.2720 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: 2.224197 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): -38.37900 16.57500 ymin,ymax (A): 3.324000 52.65700 zmin,zma (A): -3.125000 68.90100 x,y,z range (A): 54.95400 49.33300 72.02600 scale (grids/A): 2.224197 object centre (A): -10.90200 27.99050 32.88800 number of atom coordinates read : 3142 total number of charged atoms : 2991 net assigned charge : 3.228023 assigned positive charge : 463.4311 centred at (gu) : 95.90672 89.22780 85.99289 assigned negative charge : -460.2041 centred at (gu) : 96.06644 89.31879 85.78532 start vw surface at 0.1100000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 130190 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31703 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 55933 mr = 87706 m= 14250 mr = 42210 m= 1673 mr = 9936 m= 57 mr = 966 m= 0 mr = 12 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 877 time to turn everything in is 0.6900000 number of dielectric boundary points 61273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 86 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 23846 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) : 1.482798 object centre at (A) : -10.90200 27.99050 32.88800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2670748E-02 -0.1929453 midg,1,midg; midg,igrid,midg 9.2224248E-02 4.1629286E-03 1,midg,midg; igrid,midg,midg 6.8084538E-02 -2.6982822E-02 gauss-seidel spectral radius is 0.9990247 estimated iterations to convergence 253 setup time was (sec) 0.9200000 now iterating at: 09:40:15 rms-change max change #iterations 7.591820 269.0364 at 10iterations 4.155588 120.4416 at 20iterations 2.247986 60.75925 at 30iterations 1.206730 37.46368 at 40iterations 0.6451298 16.69418 at 50iterations 0.3452258 9.401480 at 60iterations 0.1833493 4.671790 at 70iterations 9.7485542E-02 2.705067 at 80iterations 5.1723201E-02 1.260437 at 90iterations 2.7365187E-02 0.6425170 at 100iterations 1.4520742E-02 0.3391914 at 110iterations 7.6805376E-03 0.1735067 at 120iterations 4.0651946E-03 0.1003456 at 130iterations 2.1501044E-03 6.3632965E-02 at 140iterations 1.1396325E-03 2.6420593E-02 at 150iterations 6.0267252E-04 1.4689445E-02 at 160iterations 3.1777617E-04 8.3770752E-03 at 170iterations 1.6906278E-04 4.2457581E-03 at 180iterations finished qdiffx linear iterations at : 09:40:26 total time elapsed so far: 11.99000 # loops : 180 mean,max change (kT/e) : 1.6906278E-04 4.2457581E-03 energy calculations done at 11.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.13000 DelPhi exited at 09:40:27 12.128u 0.183s 0:12.58 97.7% 0+0k 0+0io 0pf+0w