Sat Oct 8 13:45:50 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 Sat Oct 8 2011 at 13:45:50 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2992 !!! WARNING: HIR 110 has a net charge of 0.5140 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: 0.6403338 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): -12.15000 43.44600 ymin,ymax (A): -21.89600 22.60200 zmin,zma (A): -8.335000 46.80600 x,y,z range (A): 55.59600 44.49800 55.14100 scale (grids/A): 0.6403338 object centre (A): 15.64800 0.3529997 19.23550 number of atom coordinates read : 2992 total number of charged atoms : 2845 net assigned charge : 2.014008 assigned positive charge : 446.5287 centred at (gu) : 88.66302 89.76452 92.04539 assigned negative charge : -444.5153 centred at (gu) : 88.61977 89.70574 91.92795 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8077 nv = 96 ne = 84 npr = 62618 no. pairs analyzed = 62618 no. exposed pairs = 3414 no. arc points = 23976 no. surface atoms = 1155 nbur = 1837 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 426 mr = 4698 m= 2 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2274 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9839 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4712770E-09 2.8538018E-08 midg,1,midg; midg,igrid,midg -5.5097180E-09 1.0007316E-08 1,midg,midg; igrid,midg,midg -4.2539976E-09 6.3770131E-09 gauss-seidel spectral radius is 0.9873908 estimated iterations to convergence 73 setup time was (sec) 0.4300000 now iterating at: 13:45:51 rms-change max change #iterations 0.1571768 19.23729 at 10iterations 1.6163835E-02 2.242325 at 20iterations 1.6759809E-03 0.2197189 at 30iterations 1.8656191E-04 2.3344040E-02 at 40iterations 2.4136487E-05 3.0841827E-03 at 50iterations finished qdiffx linear iterations at : 13:45:54 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 2.4136487E-05 3.0841827E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 13:45:55 3.710u 0.204s 0:04.21 92.8% 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 Sat Oct 8 2011 at 13:45:55 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2992 !!! WARNING: HIR 110 has a net charge of 0.5140 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: 1.921001 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): -12.15000 43.44600 ymin,ymax (A): -21.89600 22.60200 zmin,zma (A): -8.335000 46.80600 x,y,z range (A): 55.59600 44.49800 55.14100 scale (grids/A): 1.921001 object centre (A): 15.64800 0.3529997 19.23550 number of atom coordinates read : 2992 total number of charged atoms : 2845 net assigned charge : 2.014008 assigned positive charge : 446.5287 centred at (gu) : 85.98848 89.29277 96.13601 assigned negative charge : -444.5153 centred at (gu) : 85.85892 89.11693 95.78348 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 87906 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23976 grid for indexing accessible points = 1.400000 m= 32215 mr = 63351 m= 4999 mr = 24330 m= 353 mr = 3274 m= 5 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 955 time to turn everything in is 0.4300000 number of dielectric boundary points 34362 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 142 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 22388 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) : 0.6403338 object centre at (A) : 15.64800 0.3529997 19.23550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4259277E-02 3.2441322E-02 midg,1,midg; midg,igrid,midg 2.8482743E-03 1.5347688E-02 1,midg,midg; igrid,midg,midg -3.2278582E-02 1.8775970E-02 gauss-seidel spectral radius is 0.9986848 estimated iterations to convergence 218 setup time was (sec) 0.6900000 now iterating at: 13:45:56 rms-change max change #iterations 4.660018 162.2906 at 10iterations 2.216692 65.79713 at 20iterations 1.056070 34.35591 at 30iterations 0.5037984 14.15138 at 40iterations 0.2388934 7.087160 at 50iterations 0.1139916 3.409582 at 60iterations 5.4259654E-02 1.637028 at 70iterations 2.5820589E-02 0.7551117 at 80iterations 1.2285168E-02 0.3493541 at 90iterations 5.8781439E-03 0.1883183 at 100iterations 2.7933153E-03 8.2272530E-02 at 110iterations 1.3363812E-03 4.3997765E-02 at 120iterations finished qdiffx linear iterations at : 13:46:04 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 1.3363812E-03 4.3997765E-02 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.350000 DelPhi exited at 13:46:05 9.354u 0.242s 0:09.89 96.9% 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 Sat Oct 8 2011 at 13:46:05 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2992 !!! WARNING: HIR 110 has a net charge of 0.5140 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: 2.881502 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): -12.15000 43.44600 ymin,ymax (A): -21.89600 22.60200 zmin,zma (A): -8.335000 46.80600 x,y,z range (A): 55.59600 44.49800 55.14100 scale (grids/A): 2.881502 object centre (A): 15.64800 0.3529997 19.23550 number of atom coordinates read : 2992 total number of charged atoms : 2845 net assigned charge : 2.014008 assigned positive charge : 446.5287 centred at (gu) : 83.98248 88.93919 99.20365 assigned negative charge : -444.5153 centred at (gu) : 83.78838 88.67535 98.67509 start vw surface at 0.1000000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 203510 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23976 grid for indexing accessible points = 1.400000 m= 104745 mr = 152888 m= 37559 mr = 87411 m= 9294 mr = 30558 m= 1511 mr = 7126 m= 123 mr = 1093 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 3169 time to turn everything in is 1.180000 number of dielectric boundary points 77613 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 22755 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) : 1.921001 object centre at (A) : 15.64800 0.3529997 19.23550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4792203E-02 0.4275939 midg,1,midg; midg,igrid,midg 3.2613561E-02 0.1692105 1,midg,midg; igrid,midg,midg -0.5167154 0.2339467 gauss-seidel spectral radius is 0.9992775 estimated iterations to convergence 294 setup time was (sec) 1.480000 now iterating at: 13:46:06 rms-change max change #iterations 10.83766 458.8306 at 10iterations 6.366828 117.4262 at 20iterations 3.723697 65.05040 at 30iterations 2.168493 40.23830 at 40iterations 1.262668 22.68001 at 50iterations 0.7340972 13.31138 at 60iterations 0.4265541 7.586163 at 70iterations 0.2470360 4.199127 at 80iterations 0.1436347 2.414917 at 90iterations 8.3163306E-02 1.305998 at 100iterations 4.8095126E-02 0.8626099 at 110iterations 2.7894823E-02 0.4416454 at 120iterations 1.6142612E-02 0.2918606 at 130iterations 9.3829613E-03 0.1558008 at 140iterations 5.4362216E-03 0.1005497 at 150iterations 3.1535451E-03 5.3110600E-02 at 160iterations 1.8348543E-03 3.3393860E-02 at 170iterations 1.0695232E-03 1.8089294E-02 at 180iterations finished qdiffx linear iterations at : 13:46:20 total time elapsed so far: 15.13000 # loops : 180 mean,max change (kT/e) : 1.0695232E-03 1.8089294E-02 energy calculations done at 15.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.25000 DelPhi exited at 13:46:20 15.252u 0.288s 0:15.83 98.1% 0+0k 0+0io 0pf+0w