Wed Feb 15 08:53:40 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:53:40 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 ! Automatically converted by prot2crg.py # of charge parameter records: 961 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1467 !!! WARNING: CYM 48 has a net charge of -0.8000 !!! WARNING: CYM 51 has a net charge of -0.8000 !!! WARNING: CYM 75 has a net charge of -0.8000 !!! WARNING: CYM 139 has a net charge of -0.8000 !!! WARNING: CYM 142 has a net charge of -0.8000 !!! WARNING: HIZ 159 has a net charge of 0.2000 !!! WARNING: ZN 185 has a net charge of 1.4000 !!! WARNING: ZN 186 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6986145 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): -24.40700 26.55100 ymin,ymax (A): -10.04600 31.52600 zmin,zma (A): -34.26300 7.560000 x,y,z range (A): 50.95800 41.57200 41.82300 scale (grids/A): 0.6986145 object centre (A): 1.072000 10.74000 -13.35150 number of atom coordinates read : 1467 total number of charged atoms : 1330 net assigned charge : -2.999996 assigned positive charge : 209.3363 centred at (gu) : 89.20085 90.44061 91.07674 assigned negative charge : -212.3362 centred at (gu) : 89.16740 90.44264 91.02173 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4896 nv = 96 ne = 84 npr = 30180 no. pairs analyzed = 30180 no. exposed pairs = 2217 no. arc points = 16139 no. surface atoms = 734 nbur = 733 mkacc time = 6.0000002E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 304 mr = 2179 m= 3 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 6.9999993E-02 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.2100000 number of dielectric boundary points 3000 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1383 ## 98 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 5380 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9031240E-08 -6.5070447E-09 midg,1,midg; midg,igrid,midg -1.8387192E-08 -2.2960986E-08 1,midg,midg; igrid,midg,midg -3.4801822E-08 -9.8488169E-09 gauss-seidel spectral radius is 0.9892758 estimated iterations to convergence 79 setup time was (sec) 0.4200000 now iterating at: 08:53:40 rms-change max change #iterations 0.1548022 25.59803 at 10iterations 1.7577559E-02 2.977858 at 20iterations 2.0732186E-03 0.3433005 at 30iterations 2.4365869E-04 3.6712646E-02 at 40iterations 2.8673947E-05 4.4403076E-03 at 50iterations finished qdiffx linear iterations at : 08:53:43 total time elapsed so far: 2.840000 # loops : 50 mean,max change (kT/e) : 2.8673947E-05 4.4403076E-03 energy calculations done at 2.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.020000 DelPhi exited at 08:53:43 3.019u 0.153s 0:03.77 83.8% 0+0k 0+0io 6pf+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 Wed Feb 15 2012 at 08:53:44 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 ! Automatically converted by prot2crg.py # of charge parameter records: 961 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1467 !!! WARNING: CYM 48 has a net charge of -0.8000 !!! WARNING: CYM 51 has a net charge of -0.8000 !!! WARNING: CYM 75 has a net charge of -0.8000 !!! WARNING: CYM 139 has a net charge of -0.8000 !!! WARNING: CYM 142 has a net charge of -0.8000 !!! WARNING: HIZ 159 has a net charge of 0.2000 !!! WARNING: ZN 185 has a net charge of 1.4000 !!! WARNING: ZN 186 has a net charge of 1.4000 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: 2.095844 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): -24.40700 26.55100 ymin,ymax (A): -10.04600 31.52600 zmin,zma (A): -34.26300 7.560000 x,y,z range (A): 50.95800 41.57200 41.82300 scale (grids/A): 2.095844 object centre (A): 1.072000 10.74000 -13.35150 number of atom coordinates read : 1467 total number of charged atoms : 1330 net assigned charge : -2.999996 assigned positive charge : 209.3363 centred at (gu) : 87.60265 91.32216 93.23043 assigned negative charge : -212.3362 centred at (gu) : 87.50235 91.32827 93.06543 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 51431 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16139 grid for indexing accessible points = 1.400000 m= 17237 mr = 31521 m= 2891 mr = 11125 m= 268 mr = 1520 m= 8 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 788 time to turn everything in is 0.4100000 number of dielectric boundary points 27602 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 10562 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) : 0.6986145 object centre at (A) : 1.072000 10.74000 -13.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1964396E-02 -1.4716619E-02 midg,1,midg; midg,igrid,midg -3.2528217E-03 -1.9871730E-02 1,midg,midg; igrid,midg,midg 2.8957846E-03 -1.6147975E-02 gauss-seidel spectral radius is 0.9987564 estimated iterations to convergence 225 setup time was (sec) 0.6700000 now iterating at: 08:53:44 rms-change max change #iterations 3.689071 200.0714 at 10iterations 1.769498 76.96950 at 20iterations 0.8579515 33.06972 at 30iterations 0.4122158 15.92318 at 40iterations 0.1992860 7.802562 at 50iterations 9.5915519E-02 4.026291 at 60iterations 4.6276230E-02 1.785053 at 70iterations 2.2309067E-02 0.8222733 at 80iterations 1.0735794E-02 0.3880800 at 90iterations 5.1673790E-03 0.1811571 at 100iterations 2.5011762E-03 0.1025982 at 110iterations 1.2070322E-03 4.3212891E-02 at 120iterations finished qdiffx linear iterations at : 08:53:50 total time elapsed so far: 6.620000 # loops : 120 mean,max change (kT/e) : 1.2070322E-03 4.3212891E-02 energy calculations done at 6.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.790000 DelPhi exited at 08:53:51 6.793u 0.169s 0:07.43 93.5% 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 Wed Feb 15 2012 at 08:53:51 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 ! Automatically converted by prot2crg.py # of charge parameter records: 961 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1467 !!! WARNING: CYM 48 has a net charge of -0.8000 !!! WARNING: CYM 51 has a net charge of -0.8000 !!! WARNING: CYM 75 has a net charge of -0.8000 !!! WARNING: CYM 139 has a net charge of -0.8000 !!! WARNING: CYM 142 has a net charge of -0.8000 !!! WARNING: HIZ 159 has a net charge of 0.2000 !!! WARNING: ZN 185 has a net charge of 1.4000 !!! WARNING: ZN 186 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.143765 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): -24.40700 26.55100 ymin,ymax (A): -10.04600 31.52600 zmin,zma (A): -34.26300 7.560000 x,y,z range (A): 50.95800 41.57200 41.82300 scale (grids/A): 3.143765 object centre (A): 1.072000 10.74000 -13.35150 number of atom coordinates read : 1467 total number of charged atoms : 1330 net assigned charge : -2.999996 assigned positive charge : 209.3363 centred at (gu) : 86.40396 91.98329 94.84586 assigned negative charge : -212.3362 centred at (gu) : 86.25358 91.99239 94.59810 start vw surface at 0.1200000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 118721 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16139 grid for indexing accessible points = 1.400000 m= 54805 mr = 77426 m= 19600 mr = 41504 m= 5105 mr = 14159 m= 957 mr = 3406 m= 94 mr = 515 m= 8 mr = 45 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 2561 time to turn everything in is 1.170000 number of dielectric boundary points 62236 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 10640 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) : 2.095844 object centre at (A) : 1.072000 10.74000 -13.35150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.6135226E-02 -0.1152687 midg,1,midg; midg,igrid,midg 1.9573113E-02 -0.2010280 1,midg,midg; igrid,midg,midg 0.1218701 -0.2308151 gauss-seidel spectral radius is 0.9992957 estimated iterations to convergence 297 setup time was (sec) 1.430000 now iterating at: 08:53:54 rms-change max change #iterations 8.474817 417.8678 at 10iterations 5.052239 156.1456 at 20iterations 2.998648 72.63379 at 30iterations 1.774053 41.02432 at 40iterations 1.037916 23.60487 at 50iterations 0.6098989 13.54677 at 60iterations 0.3567227 7.645775 at 70iterations 0.2085905 4.470126 at 80iterations 0.1213702 2.578770 at 90iterations 7.0869707E-02 1.642058 at 100iterations 4.1130953E-02 1.001171 at 110iterations 2.3977958E-02 0.5403519 at 120iterations 1.3920285E-02 0.3168468 at 130iterations 8.1058284E-03 0.1880634 at 140iterations 4.7090175E-03 0.1119623 at 150iterations 2.7332888E-03 5.4128647E-02 at 160iterations 1.5867354E-03 3.4327030E-02 at 170iterations 9.2350377E-04 2.0362854E-02 at 180iterations finished qdiffx linear iterations at : 08:54:03 total time elapsed so far: 10.77000 # loops : 180 mean,max change (kT/e) : 9.2350377E-04 2.0362854E-02 energy calculations done at 10.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.95000 DelPhi exited at 08:54:04 10.950u 0.189s 0:13.31 83.6% 0+0k 0+0io 0pf+0w