Sun Jan 29 13:39:49 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.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 Jan 29 2012 at 13:39:49 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: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3792 !!! WARNING: DIC 170 has a net charge of -0.8000 !!! WARNING: HIY 172 has a net charge of 0.2000 !!! WARNING: DIC 258 has a net charge of -0.8000 !!! WARNING: ZN 1098 has a net charge of 1.4000 !!! WARNING: CA 1099 has a net charge of 2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5712451 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): 32.59500 94.91500 ymin,ymax (A): -2.061000 56.44800 zmin,zma (A): -32.60900 27.25900 x,y,z range (A): 62.32000 58.50900 59.86800 scale (grids/A): 0.5712451 object centre (A): 63.75500 27.19350 -2.675000 number of atom coordinates read : 3792 total number of charged atoms : 3673 net assigned charge : 5.000020 assigned positive charge : 585.3239 centred at (gu) : 88.21684 89.61327 90.38301 assigned negative charge : -580.3262 centred at (gu) : 88.31611 89.67448 90.44369 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7901 nv = 96 ne = 84 npr = 77146 no. pairs analyzed = 77146 no. exposed pairs = 4367 no. arc points = 30374 no. surface atoms = 1478 nbur = 2314 mkacc time = 0.1600000 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 = 1.512000 m= 328 mr = 4481 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3725 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3180 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 10400 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8664177E-09 -6.0299782E-10 midg,1,midg; midg,igrid,midg 2.2521804E-09 -5.0432142E-10 1,midg,midg; igrid,midg,midg 4.3815458E-09 -8.9321583E-10 gauss-seidel spectral radius is 0.9842404 estimated iterations to convergence 65 setup time was (sec) 0.5300000 now iterating at: 13:39:49 rms-change max change #iterations 0.1045766 14.46344 at 10iterations 8.0116820E-03 1.044956 at 20iterations 6.8581291E-04 0.1069298 at 30iterations 1.1789717E-04 1.6495468E-02 at 40iterations 3.4423094E-05 5.4543018E-03 at 50iterations finished qdiffx linear iterations at : 13:39:52 total time elapsed so far: 3.470000 # loops : 50 mean,max change (kT/e) : 3.4423094E-05 5.4543018E-03 energy calculations done at 3.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 13:39:53 3.621u 0.177s 0:04.08 92.8% 0+0k 0+46176io 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 Jan 29 2012 at 13:39:53 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: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3792 !!! WARNING: DIC 170 has a net charge of -0.8000 !!! WARNING: HIY 172 has a net charge of 0.2000 !!! WARNING: DIC 258 has a net charge of -0.8000 !!! WARNING: ZN 1098 has a net charge of 1.4000 !!! WARNING: CA 1099 has a net charge of 2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.713735 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): 32.59500 94.91500 ymin,ymax (A): -2.061000 56.44800 zmin,zma (A): -32.60900 27.25900 x,y,z range (A): 62.32000 58.50900 59.86800 scale (grids/A): 1.713735 object centre (A): 63.75500 27.19350 -2.675000 number of atom coordinates read : 3792 total number of charged atoms : 3673 net assigned charge : 5.000020 assigned positive charge : 585.3239 centred at (gu) : 84.64906 88.83860 91.14748 assigned negative charge : -580.3262 centred at (gu) : 84.94781 89.02290 91.33069 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 88376 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30374 grid for indexing accessible points = 1.400000 m= 27742 mr = 63206 m= 3087 mr = 20122 m= 92 mr = 1672 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 561 time to turn everything in is 0.5200000 number of dielectric boundary points 34282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 324 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 28406 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) : 0.5712451 object centre at (A) : 63.75500 27.19350 -2.675000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3423798E-02 -1.5366942E-02 midg,1,midg; midg,igrid,midg 2.1971608E-02 9.4375052E-03 1,midg,midg; igrid,midg,midg 2.5064243E-02 -9.7321505E-03 gauss-seidel spectral radius is 0.9984198 estimated iterations to convergence 200 setup time was (sec) 0.7200000 now iterating at: 13:39:54 rms-change max change #iterations 4.316204 163.1019 at 10iterations 1.906858 61.90331 at 20iterations 0.8420737 25.81070 at 30iterations 0.3737802 12.19352 at 40iterations 0.1652297 5.242523 at 50iterations 7.3192164E-02 2.411455 at 60iterations 3.2416970E-02 1.007048 at 70iterations 1.4356740E-02 0.4183121 at 80iterations 6.3990518E-03 0.2156029 at 90iterations 2.8675920E-03 8.8472366E-02 at 100iterations 1.2903145E-03 3.9914608E-02 at 110iterations 5.8947009E-04 1.7574310E-02 at 120iterations finished qdiffx linear iterations at : 13:40:01 total time elapsed so far: 7.990000 # loops : 120 mean,max change (kT/e) : 5.8947009E-04 1.7574310E-02 energy calculations done at 7.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.130000 DelPhi exited at 13:40:01 8.140u 0.210s 0:08.67 96.3% 0+0k 0+45440io 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 Jan 29 2012 at 13:40:02 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 ! Automatically converted by prot2crg.py # of charge parameter records: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3792 !!! WARNING: DIC 170 has a net charge of -0.8000 !!! WARNING: HIY 172 has a net charge of 0.2000 !!! WARNING: DIC 258 has a net charge of -0.8000 !!! WARNING: ZN 1098 has a net charge of 1.4000 !!! WARNING: CA 1099 has a net charge of 2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.570603 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): 32.59500 94.91500 ymin,ymax (A): -2.061000 56.44800 zmin,zma (A): -32.60900 27.25900 x,y,z range (A): 62.32000 58.50900 59.86800 scale (grids/A): 2.570603 object centre (A): 63.75500 27.19350 -2.675000 number of atom coordinates read : 3792 total number of charged atoms : 3673 net assigned charge : 5.000020 assigned positive charge : 585.3239 centred at (gu) : 81.97343 88.25751 91.72104 assigned negative charge : -580.3262 centred at (gu) : 82.42160 88.53419 91.99583 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 205960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30374 grid for indexing accessible points = 1.400000 m= 96821 mr = 154090 m= 27851 mr = 79033 m= 4987 mr = 21835 m= 431 mr = 3521 m= 11 mr = 238 m= 0 mr = 4 time to grow re-entrant surface = 0.8399999 no. cavity mid-points inaccessible to solvent = 1692 time to turn everything in is 1.310000 number of dielectric boundary points 77340 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 29374 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) : 1.713735 object centre at (A) : 63.75500 27.19350 -2.675000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8972665 -0.2995094 midg,1,midg; midg,igrid,midg 0.3640162 0.1415608 1,midg,midg; igrid,midg,midg 3.5199899E-02 -0.1245681 gauss-seidel spectral radius is 0.9992135 estimated iterations to convergence 282 setup time was (sec) 1.540000 now iterating at: 13:40:03 rms-change max change #iterations 10.56019 392.5873 at 10iterations 6.035005 154.6547 at 20iterations 3.446919 84.36736 at 30iterations 1.961829 45.46844 at 40iterations 1.113708 21.92699 at 50iterations 0.6321102 11.65784 at 60iterations 0.3587176 6.876577 at 70iterations 0.2027932 3.941259 at 80iterations 0.1149517 2.094002 at 90iterations 6.4903125E-02 1.159515 at 100iterations 3.6807440E-02 0.6572771 at 110iterations 2.0811211E-02 0.3888321 at 120iterations 1.1769197E-02 0.2099037 at 130iterations 6.6665905E-03 0.1156905 at 140iterations 3.7916773E-03 6.6627502E-02 at 150iterations 2.1647902E-03 3.6949158E-02 at 160iterations 1.2427118E-03 2.2191048E-02 at 170iterations 7.2380906E-04 1.2969971E-02 at 180iterations finished qdiffx linear iterations at : 13:40:15 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 7.2380906E-04 1.2969971E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 13:40:15 13.175u 0.234s 0:13.70 97.8% 0+0k 0+45432io 0pf+0w