Sun Oct 9 14:39:26 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 Sun Oct 9 2011 at 14:39:27 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1373 !!! WARNING: GLM 95 has a net charge of -0.0940 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: 0.8499057 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): -9.937000 24.54200 ymin,ymax (A): -9.076000 30.65200 zmin,zma (A): -6.478000 35.40900 x,y,z range (A): 34.47900 39.72800 41.88700 scale (grids/A): 0.8499057 object centre (A): 7.302500 10.78800 14.46550 number of atom coordinates read : 1373 total number of charged atoms : 1249 net assigned charge : -0.5939968 assigned positive charge : 205.5693 centred at (gu) : 90.35770 88.62750 90.83187 assigned negative charge : -206.1631 centred at (gu) : 90.40022 88.73709 90.50320 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6772 nv = 96 ne = 84 npr = 29749 no. pairs analyzed = 29749 no. exposed pairs = 1707 no. arc points = 12500 no. surface atoms = 575 nbur = 798 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 608 mr = 3795 m= 10 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.1400000 number of dielectric boundary points 3453 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 810 ## 68 charges are in solution ## iepsmp to db, and charging done at 0.2000000 number of grid points assigned charge 6323 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4413456E-06 1.5810239E-06 midg,1,midg; midg,igrid,midg 5.0598629E-07 -4.8594393E-07 1,midg,midg; igrid,midg,midg 8.7578002E-08 -3.1679096E-07 gauss-seidel spectral radius is 0.9926933 estimated iterations to convergence 95 setup time was (sec) 0.3200000 now iterating at: 14:39:27 rms-change max change #iterations 0.3352911 47.27513 at 10iterations 5.7578765E-02 6.677155 at 20iterations 9.9756308E-03 1.282059 at 30iterations 1.6905479E-03 0.2283077 at 40iterations 2.9510245E-04 4.0748596E-02 at 50iterations finished qdiffx linear iterations at : 14:39:30 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 2.9510245E-04 4.0748596E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 14:39:30 3.339u 0.171s 0:03.78 92.5% 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 Sun Oct 9 2011 at 14:39:30 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1373 !!! WARNING: GLM 95 has a net charge of -0.0940 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: 2.549717 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): -9.937000 24.54200 ymin,ymax (A): -9.076000 30.65200 zmin,zma (A): -6.478000 35.40900 x,y,z range (A): 34.47900 39.72800 41.88700 scale (grids/A): 2.549717 object centre (A): 7.302500 10.78800 14.46550 number of atom coordinates read : 1373 total number of charged atoms : 1249 net assigned charge : -0.5939968 assigned positive charge : 205.5693 centred at (gu) : 91.07322 85.88288 92.49586 assigned negative charge : -206.1631 centred at (gu) : 91.20063 86.21133 91.50955 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12500 grid for indexing accessible points = 1.400000 m= 29553 mr = 47652 m= 7672 mr = 22885 m= 1267 mr = 5405 m= 153 mr = 749 m= 7 mr = 95 m= 0 mr = 4 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1182 time to turn everything in is 0.3800000 number of dielectric boundary points 31434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9985 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) : 0.8499057 object centre at (A) : 7.302500 10.78800 14.46550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8677160E-02 9.3814962E-02 midg,1,midg; midg,igrid,midg 1.4339708E-02 -7.0963323E-02 1,midg,midg; igrid,midg,midg -1.5134112E-02 7.3777656E-03 gauss-seidel spectral radius is 0.9990711 estimated iterations to convergence 259 setup time was (sec) 0.5900000 now iterating at: 14:39:31 rms-change max change #iterations 5.067959 278.3744 at 10iterations 2.708879 106.3298 at 20iterations 1.445295 40.08050 at 30iterations 0.7726216 26.84388 at 40iterations 0.4140013 15.27517 at 50iterations 0.2215240 6.188484 at 60iterations 0.1183259 3.331768 at 70iterations 6.3352861E-02 1.877780 at 80iterations 3.3637419E-02 0.9300184 at 90iterations 1.8063365E-02 0.5577011 at 100iterations 9.6495803E-03 0.2987843 at 110iterations 5.1508220E-03 0.1411095 at 120iterations finished qdiffx linear iterations at : 14:39:38 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 5.1508220E-03 0.1411095 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.850000 DelPhi exited at 14:39:39 7.855u 0.202s 0:08.36 96.2% 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 Sun Oct 9 2011 at 14:39:39 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1373 !!! WARNING: GLM 95 has a net charge of -0.0940 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: 3.824576 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): -9.937000 24.54200 ymin,ymax (A): -9.076000 30.65200 zmin,zma (A): -6.478000 35.40900 x,y,z range (A): 34.47900 39.72800 41.88700 scale (grids/A): 3.824576 object centre (A): 7.302500 10.78800 14.46550 number of atom coordinates read : 1373 total number of charged atoms : 1249 net assigned charge : -0.5939968 assigned positive charge : 205.5693 centred at (gu) : 91.60994 83.82417 93.74387 assigned negative charge : -206.1631 centred at (gu) : 91.80096 84.31700 92.26425 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 159762 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12500 grid for indexing accessible points = 1.400000 m= 87575 mr = 114322 m= 41341 mr = 73303 m= 15464 mr = 34847 m= 4429 mr = 12341 m= 1175 mr = 3258 m= 235 mr = 914 m= 18 mr = 172 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 3973 time to turn everything in is 1.180000 number of dielectric boundary points 70829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 9988 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) : 2.549717 object centre at (A) : 7.302500 10.78800 14.46550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1159227 0.5338562 midg,1,midg; midg,igrid,midg 0.1055772 -0.5374119 1,midg,midg; igrid,midg,midg -0.1529665 0.1392961 gauss-seidel spectral radius is 0.9993379 estimated iterations to convergence 307 setup time was (sec) 1.410000 now iterating at: 14:39:40 rms-change max change #iterations 10.35808 273.2269 at 10iterations 6.144410 135.5128 at 20iterations 3.628551 69.42856 at 30iterations 2.143722 39.74384 at 40iterations 1.267208 22.93130 at 50iterations 0.7508338 12.30256 at 60iterations 0.4439912 6.965771 at 70iterations 0.2618158 4.742088 at 80iterations 0.1551178 2.568810 at 90iterations 9.1680460E-02 1.472065 at 100iterations 5.4360237E-02 1.072948 at 110iterations 3.2219850E-02 0.5895553 at 120iterations 1.9061143E-02 0.3257217 at 130iterations 1.1321390E-02 0.1967392 at 140iterations 6.7723840E-03 0.1078262 at 150iterations 4.0531824E-03 6.9892883E-02 at 160iterations 2.4596683E-03 4.3323517E-02 at 170iterations 1.5200689E-03 2.8221130E-02 at 180iterations finished qdiffx linear iterations at : 14:39:53 total time elapsed so far: 13.53000 # loops : 180 mean,max change (kT/e) : 1.5200689E-03 2.8221130E-02 energy calculations done at 13.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.65000 DelPhi exited at 14:39:53 13.655u 0.248s 0:14.21 97.7% 0+0k 0+0io 0pf+0w