Tue Oct 11 08:32:48 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 Tue Oct 11 2011 at 08:32:48 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2116 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 195 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7187853 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): -8.488000 38.40700 ymin,ymax (A): -30.12200 19.40600 zmin,zma (A): 3.758000 46.38800 x,y,z range (A): 46.89500 49.52800 42.63000 scale (grids/A): 0.7187853 object centre (A): 14.95950 -5.358000 25.07300 number of atom coordinates read : 2116 total number of charged atoms : 1986 net assigned charge : 6.039011 assigned positive charge : 327.1161 centred at (gu) : 90.60156 89.24937 90.31703 assigned negative charge : -321.0771 centred at (gu) : 90.47694 89.30476 90.42635 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7479 nv = 96 ne = 84 npr = 42319 no. pairs analyzed = 42319 no. exposed pairs = 2522 no. arc points = 17244 no. surface atoms = 864 nbur = 1252 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 508 mr = 4403 m= 1 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3500 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1541 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8138 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2838747E-07 -6.9754664E-09 midg,1,midg; midg,igrid,midg 1.1736589E-07 2.5954144E-08 1,midg,midg; igrid,midg,midg -1.4251247E-08 1.6406921E-07 gauss-seidel spectral radius is 0.9899108 estimated iterations to convergence 81 setup time was (sec) 0.3400000 now iterating at: 08:32:48 rms-change max change #iterations 0.2191969 39.50362 at 10iterations 2.8703161E-02 3.794858 at 20iterations 3.8062804E-03 0.5156498 at 30iterations 6.2129379E-04 8.8932037E-02 at 40iterations 1.5481541E-04 1.9857407E-02 at 50iterations finished qdiffx linear iterations at : 08:32:51 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 1.5481541E-04 1.9857407E-02 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 08:32:52 3.342u 0.192s 0:03.86 91.4% 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 Tue Oct 11 2011 at 08:32:52 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2116 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 195 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.156356 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): -8.488000 38.40700 ymin,ymax (A): -30.12200 19.40600 zmin,zma (A): 3.758000 46.38800 x,y,z range (A): 46.89500 49.52800 42.63000 scale (grids/A): 2.156356 object centre (A): 14.95950 -5.358000 25.07300 number of atom coordinates read : 2116 total number of charged atoms : 1986 net assigned charge : 6.039011 assigned positive charge : 327.1161 centred at (gu) : 91.80480 87.74817 90.95090 assigned negative charge : -321.0771 centred at (gu) : 91.43107 87.91434 91.27924 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79287 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17244 grid for indexing accessible points = 1.400000 m= 32847 mr = 57043 m= 6450 mr = 25302 m= 547 mr = 4326 m= 16 mr = 279 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 32197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15790 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) : 0.7187853 object centre at (A) : 14.95950 -5.358000 25.07300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6483675E-02 2.0270254E-02 midg,1,midg; midg,igrid,midg 4.3890901E-02 3.1298220E-02 1,midg,midg; igrid,midg,midg -4.5205154E-02 3.6362704E-02 gauss-seidel spectral radius is 0.9988656 estimated iterations to convergence 235 setup time was (sec) 0.6300000 now iterating at: 08:32:52 rms-change max change #iterations 4.872416 196.3947 at 10iterations 2.423924 86.17358 at 20iterations 1.221006 37.84542 at 30iterations 0.6124968 19.13006 at 40iterations 0.3073815 9.201460 at 50iterations 0.1538950 4.270602 at 60iterations 7.7375531E-02 2.281460 at 70iterations 3.8943455E-02 1.076653 at 80iterations 1.9673128E-02 0.6390877 at 90iterations 9.9749062E-03 0.3196335 at 100iterations 5.1103770E-03 0.1724586 at 110iterations 2.6654825E-03 7.7529907E-02 at 120iterations finished qdiffx linear iterations at : 08:33:00 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.6654825E-03 7.7529907E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 08:33:00 7.941u 0.225s 0:08.63 94.5% 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 Tue Oct 11 2011 at 08:33:00 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2116 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 195 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.234534 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): -8.488000 38.40700 ymin,ymax (A): -30.12200 19.40600 zmin,zma (A): 3.758000 46.38800 x,y,z range (A): 46.89500 49.52800 42.63000 scale (grids/A): 3.234534 object centre (A): 14.95950 -5.358000 25.07300 number of atom coordinates read : 2116 total number of charged atoms : 1986 net assigned charge : 6.039011 assigned positive charge : 327.1161 centred at (gu) : 92.70715 86.62234 91.42639 assigned negative charge : -321.0771 centred at (gu) : 92.14650 86.87152 91.91885 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 182728 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17244 grid for indexing accessible points = 1.400000 m= 101682 mr = 137054 m= 42509 mr = 85397 m= 12188 mr = 35265 m= 2325 mr = 9595 m= 286 mr = 1640 m= 8 mr = 171 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 72604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 15888 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) : 2.156356 object centre at (A) : 14.95950 -5.358000 25.07300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1313589 0.1592602 midg,1,midg; midg,igrid,midg 0.3023558 0.1834338 1,midg,midg; igrid,midg,midg -0.4863604 0.3070700 gauss-seidel spectral radius is 0.9993056 estimated iterations to convergence 299 setup time was (sec) 1.450000 now iterating at: 08:33:02 rms-change max change #iterations 10.79481 455.6621 at 10iterations 6.399202 151.9118 at 20iterations 3.799741 78.21785 at 30iterations 2.255847 46.71984 at 40iterations 1.332822 25.40318 at 50iterations 0.7854715 13.21000 at 60iterations 0.4639184 7.704135 at 70iterations 0.2731469 5.152948 at 80iterations 0.1608053 2.765184 at 90iterations 9.4835147E-02 1.608032 at 100iterations 5.5816900E-02 0.9470863 at 110iterations 3.3051122E-02 0.5731335 at 120iterations 1.9654971E-02 0.3609314 at 130iterations 1.1839765E-02 0.2243919 at 140iterations 7.2958251E-03 0.1286469 at 150iterations 4.6465308E-03 8.1836700E-02 at 160iterations 3.1131357E-03 5.5374146E-02 at 170iterations 2.2148832E-03 4.2205811E-02 at 180iterations finished qdiffx linear iterations at : 08:33:13 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 2.2148832E-03 4.2205811E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.95000 DelPhi exited at 08:33:14 12.951u 0.203s 0:13.59 96.7% 0+0k 0+0io 0pf+0w