Thu Jan 19 13:34:23 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+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 Thu Jan 19 2012 at 13:34:25 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6736 !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: LYS 690 has a net charge of 0.0730 !!! WARNING: LYS 691 has a net charge of 0.0730 !!! WARNING: GLN 692 has a net charge of 0.0170 !!! WARNING: ARG 701 has a net charge of 0.0400 !!! WARNING: LYS 708 has a net charge of 0.0200 !!! WARNING: LYS 770 has a net charge of 0.0200 !!! WARNING: ARG 799 has a net charge of 0.0400 !!! WARNING: LYS 839 has a net charge of 0.0200 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: ARG 918 has a net charge of 0.0400 !!! WARNING: LYS 975 has a net charge of 0.0200 !!! WARNING: ARG 981 has a net charge of 0.0400 !!! WARNING: LYS 995 has a net charge of 0.0200 !!! WARNING: LYS 1007 has a net charge of 0.0200 !!! WARNING: MET 1009 has a net charge of -0.0720 !!! WARNING: HEM 1106 has a net charge of -4.0000 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: 0.4319025 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): -3.458000 62.13400 ymin,ymax (A): -96.20300 -17.75300 zmin,zma (A): -14.33700 68.08900 x,y,z range (A): 65.59200 78.45000 82.42600 scale (grids/A): 0.4319025 object centre (A): 29.33800 -56.97800 26.87600 number of atom coordinates read : 6736 total number of charged atoms : 6586 net assigned charge : -8.388950 assigned positive charge : 1018.037 centred at (gu) : 88.61484 89.95038 91.93275 assigned negative charge : -1026.436 centred at (gu) : 88.64027 89.90585 91.97861 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7684 nv = 96 ne = 84 npr = 133777 no. pairs analyzed = 133777 no. exposed pairs = 8887 no. arc points = 60986 no. surface atoms = 2979 nbur = 3757 mkacc time = 0.2300000 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 = 1.932000 m= 205 mr = 3690 m= 0 mr = 2 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 4197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5022 ## 1016 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10457 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0053989E-13 -9.2110399E-12 midg,1,midg; midg,igrid,midg -5.0278020E-12 1.2026369E-12 1,midg,midg; igrid,midg,midg -8.6647140E-14 -2.3732121E-12 gauss-seidel spectral radius is 0.9728017 estimated iterations to convergence 51 setup time was (sec) 0.6600000 now iterating at: 13:34:29 rms-change max change #iterations 3.1912733E-02 5.941634 at 10iterations 2.4798661E-03 0.4107094 at 20iterations 8.3120482E-04 0.1378593 at 30iterations 3.0853669E-04 5.0376892E-02 at 40iterations 1.1480192E-04 1.8604279E-02 at 50iterations finished qdiffx linear iterations at : 13:34:39 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 1.1480192E-04 1.8604279E-02 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 13:34:39 4.061u 0.229s 0:14.71 29.0% 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 Thu Jan 19 2012 at 13:34:39 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6736 !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: LYS 690 has a net charge of 0.0730 !!! WARNING: LYS 691 has a net charge of 0.0730 !!! WARNING: GLN 692 has a net charge of 0.0170 !!! WARNING: ARG 701 has a net charge of 0.0400 !!! WARNING: LYS 708 has a net charge of 0.0200 !!! WARNING: LYS 770 has a net charge of 0.0200 !!! WARNING: ARG 799 has a net charge of 0.0400 !!! WARNING: LYS 839 has a net charge of 0.0200 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: ARG 918 has a net charge of 0.0400 !!! WARNING: LYS 975 has a net charge of 0.0200 !!! WARNING: ARG 981 has a net charge of 0.0400 !!! WARNING: LYS 995 has a net charge of 0.0200 !!! WARNING: LYS 1007 has a net charge of 0.0200 !!! WARNING: MET 1009 has a net charge of -0.0720 !!! WARNING: HEM 1106 has a net charge of -4.0000 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: 1.295708 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): -3.458000 62.13400 ymin,ymax (A): -96.20300 -17.75300 zmin,zma (A): -14.33700 68.08900 x,y,z range (A): 65.59200 78.45000 82.42600 scale (grids/A): 1.295708 object centre (A): 29.33800 -56.97800 26.87600 number of atom coordinates read : 6736 total number of charged atoms : 6586 net assigned charge : -8.388950 assigned positive charge : 1018.037 centred at (gu) : 85.84273 89.84854 95.79590 assigned negative charge : -1026.436 centred at (gu) : 85.92046 89.71700 95.93517 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 90285 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60986 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 21181 mr = 59993 m= 1014 mr = 12676 m= 9 mr = 244 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 313 time to turn everything in is 0.4700000 number of dielectric boundary points 39576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1034 ## 39 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 45850 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) : 0.4319025 object centre at (A) : 29.33800 -56.97800 26.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.5289677E-04 4.4493559E-03 midg,1,midg; midg,igrid,midg -3.0006645E-03 -7.4800581E-04 1,midg,midg; igrid,midg,midg -1.0332979E-03 -1.4960541E-03 gauss-seidel spectral radius is 0.9974369 estimated iterations to convergence 157 setup time was (sec) 0.6900000 now iterating at: 13:34:40 rms-change max change #iterations 3.083122 137.8476 at 10iterations 1.088241 36.74280 at 20iterations 0.3873373 13.64245 at 30iterations 0.1370012 4.526333 at 40iterations 4.8650075E-02 1.732828 at 50iterations 1.7526589E-02 0.6364937 at 60iterations 6.4367787E-03 0.2437973 at 70iterations 2.5357537E-03 9.5487595E-02 at 80iterations 1.1817788E-03 4.3340683E-02 at 90iterations 6.7350722E-04 2.4656296E-02 at 100iterations 4.3413037E-04 1.5219688E-02 at 110iterations 2.9312330E-04 9.6241236E-03 at 120iterations finished qdiffx linear iterations at : 13:34:55 total time elapsed so far: 8.300000 # loops : 120 mean,max change (kT/e) : 2.9312330E-04 9.6241236E-03 energy calculations done at 8.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.430000 DelPhi exited at 13:34:56 8.431u 0.242s 0:16.28 53.2% 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 Thu Jan 19 2012 at 13:34:56 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: 361 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6736 !!! WARNING: ARG 601 has a net charge of 0.0400 !!! WARNING: LYS 690 has a net charge of 0.0730 !!! WARNING: LYS 691 has a net charge of 0.0730 !!! WARNING: GLN 692 has a net charge of 0.0170 !!! WARNING: ARG 701 has a net charge of 0.0400 !!! WARNING: LYS 708 has a net charge of 0.0200 !!! WARNING: LYS 770 has a net charge of 0.0200 !!! WARNING: ARG 799 has a net charge of 0.0400 !!! WARNING: LYS 839 has a net charge of 0.0200 !!! WARNING: HIZ 910 has a net charge of 0.2000 !!! WARNING: ARG 918 has a net charge of 0.0400 !!! WARNING: LYS 975 has a net charge of 0.0200 !!! WARNING: ARG 981 has a net charge of 0.0400 !!! WARNING: LYS 995 has a net charge of 0.0200 !!! WARNING: LYS 1007 has a net charge of 0.0200 !!! WARNING: MET 1009 has a net charge of -0.0720 !!! WARNING: HEM 1106 has a net charge of -4.0000 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: 1.943561 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): -3.458000 62.13400 ymin,ymax (A): -96.20300 -17.75300 zmin,zma (A): -14.33700 68.08900 x,y,z range (A): 65.59200 78.45000 82.42600 scale (grids/A): 1.943561 object centre (A): 29.33800 -56.97800 26.87600 number of atom coordinates read : 6736 total number of charged atoms : 6586 net assigned charge : -8.388950 assigned positive charge : 1018.037 centred at (gu) : 83.76353 89.77233 98.69332 assigned negative charge : -1026.436 centred at (gu) : 83.88053 89.57539 98.90273 start vw surface at 0.1600000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 211659 reading accessible surface arcs data from file ARCDAT no. of arc points read = 60986 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 82620 mr = 149780 m= 14966 mr = 61062 m= 1060 mr = 9468 m= 27 mr = 434 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 1144 time to turn everything in is 1.100000 number of dielectric boundary points 89588 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 302 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 51993 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) : 1.295708 object centre at (A) : 29.33800 -56.97800 26.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9573660E-02 0.5269741 midg,1,midg; midg,igrid,midg -9.8726742E-02 -2.6973095E-02 1,midg,midg; igrid,midg,midg 1.6720503E-03 -4.1640703E-02 gauss-seidel spectral radius is 0.9989914 estimated iterations to convergence 249 setup time was (sec) 1.380000 now iterating at: 13:34:58 rms-change max change #iterations 9.445838 299.2072 at 10iterations 5.145068 130.6574 at 20iterations 2.769428 64.64640 at 30iterations 1.483804 36.75502 at 40iterations 0.7910548 22.89331 at 50iterations 0.4211929 10.35865 at 60iterations 0.2231886 4.933294 at 70iterations 0.1179455 2.577316 at 80iterations 6.2285800E-02 1.400421 at 90iterations 3.2807123E-02 0.7045741 at 100iterations 1.7309882E-02 0.3581085 at 110iterations 9.1157090E-03 0.2000275 at 120iterations 4.8059816E-03 0.1076584 at 130iterations 2.5437889E-03 5.4584503E-02 at 140iterations 1.3539634E-03 2.6838303E-02 at 150iterations 7.3352095E-04 1.5832901E-02 at 160iterations 4.0826260E-04 8.3732605E-03 at 170iterations 2.3787921E-04 5.3062439E-03 at 180iterations finished qdiffx linear iterations at : 13:35:34 total time elapsed so far: 13.45000 # loops : 180 mean,max change (kT/e) : 2.3787921E-04 5.3062439E-03 energy calculations done at 13.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.58000 DelPhi exited at 13:35:35 13.586u 0.257s 0:39.32 35.1% 0+0k 0+0io 0pf+0w