Mon Oct 10 12:11:20 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+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 Mon Oct 10 2011 at 12:11:20 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7427034 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): 9.698000 56.25100 ymin,ymax (A): -9.043000 36.10600 zmin,zma (A): -3.383000 44.55000 x,y,z range (A): 46.55300 45.14900 47.93300 scale (grids/A): 0.7427034 object centre (A): 32.97450 13.53150 20.58350 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 88.91483 90.70187 89.91824 assigned negative charge : -323.3720 centred at (gu) : 88.92116 90.79367 90.10959 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8107 nv = 96 ne = 84 npr = 43483 no. pairs analyzed = 43483 no. exposed pairs = 2740 no. arc points = 19223 no. surface atoms = 925 nbur = 1192 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 590 mr = 4509 m= 5 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2800000 number of dielectric boundary points 4064 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1546 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8395 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8693497E-08 -3.2234465E-07 midg,1,midg; midg,igrid,midg -1.6340438E-08 -2.4672684E-07 1,midg,midg; igrid,midg,midg -1.3299088E-07 -1.0138743E-07 gauss-seidel spectral radius is 0.9905543 estimated iterations to convergence 84 setup time was (sec) 0.5300000 now iterating at: 12:11:21 rms-change max change #iterations 0.2507972 34.19714 at 10iterations 3.3332072E-02 4.766051 at 20iterations 4.5855576E-03 0.5949054 at 30iterations 6.1886798E-04 7.3669434E-02 at 40iterations 8.4086896E-05 1.0344982E-02 at 50iterations finished qdiffx linear iterations at : 12:11:23 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 8.4086896E-05 1.0344982E-02 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 12:11:24 3.301u 0.195s 0:04.21 82.8% 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 Mon Oct 10 2011 at 12:11:24 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.228110 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): 9.698000 56.25100 ymin,ymax (A): -9.043000 36.10600 zmin,zma (A): -3.383000 44.55000 x,y,z range (A): 46.55300 45.14900 47.93300 scale (grids/A): 2.228110 object centre (A): 32.97450 13.53150 20.58350 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 86.74471 92.10567 89.75455 assigned negative charge : -323.3720 centred at (gu) : 86.76346 92.38103 90.32882 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19223 grid for indexing accessible points = 1.400000 m= 34684 mr = 58179 m= 7562 mr = 26608 m= 750 mr = 5286 m= 26 mr = 437 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 743 time to turn everything in is 0.6200000 number of dielectric boundary points 36933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 15755 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) : 0.7427034 object centre at (A) : 32.97450 13.53150 20.58350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.9865422E-03 -0.1175523 midg,1,midg; midg,igrid,midg -2.6332708E-02 -4.3720197E-02 1,midg,midg; igrid,midg,midg -1.9141944E-02 -2.6275928E-04 gauss-seidel spectral radius is 0.9989328 estimated iterations to convergence 242 setup time was (sec) 0.9200000 now iterating at: 12:11:26 rms-change max change #iterations 5.112420 203.8065 at 10iterations 2.595498 82.21887 at 20iterations 1.326696 38.34332 at 30iterations 0.6789885 20.58078 at 40iterations 0.3455193 12.49102 at 50iterations 0.1771821 4.764160 at 60iterations 9.0418011E-02 2.587065 at 70iterations 4.6255767E-02 1.256063 at 80iterations 2.3582479E-02 0.6621318 at 90iterations 1.2084923E-02 0.3431281 at 100iterations 6.1696712E-03 0.1811028 at 110iterations 3.1555081E-03 9.5816612E-02 at 120iterations finished qdiffx linear iterations at : 12:11:32 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 3.1555081E-03 9.5816612E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 12:11:33 7.572u 0.230s 0:08.19 95.2% 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 Mon Oct 10 2011 at 12:11:33 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.342165 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): 9.698000 56.25100 ymin,ymax (A): -9.043000 36.10600 zmin,zma (A): -3.383000 44.55000 x,y,z range (A): 46.55300 45.14900 47.93300 scale (grids/A): 3.342165 object centre (A): 32.97450 13.53150 20.58350 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 85.11700 93.15858 89.63187 assigned negative charge : -323.3720 centred at (gu) : 85.14515 93.57150 90.49320 start vw surface at 0.1400000 fill in re-entrant regions at 0.8900000 boundary points on vw surface= 193960 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19223 grid for indexing accessible points = 1.400000 m= 105136 mr = 139651 m= 46444 mr = 87622 m= 14693 mr = 38922 m= 3134 mr = 11708 m= 439 mr = 2357 m= 19 mr = 278 m= 0 mr = 4 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 2335 time to turn everything in is 2.000000 number of dielectric boundary points 83283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.140000 number of grid points assigned charge 15824 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) : 2.228110 object centre at (A) : 32.97450 13.53150 20.58350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1327580 -1.093286 midg,1,midg; midg,igrid,midg -0.2256792 -0.1854648 1,midg,midg; igrid,midg,midg -0.2496893 -4.0015135E-02 gauss-seidel spectral radius is 0.9993212 estimated iterations to convergence 303 setup time was (sec) 2.310000 now iterating at: 12:11:35 rms-change max change #iterations 11.03883 286.5226 at 10iterations 6.523331 129.5055 at 20iterations 3.849574 73.29207 at 30iterations 2.268234 40.78185 at 40iterations 1.337382 21.72154 at 50iterations 0.7886083 14.35720 at 60iterations 0.4639655 8.147046 at 70iterations 0.2730140 4.468527 at 80iterations 0.1605032 2.513813 at 90iterations 9.4489537E-02 1.618857 at 100iterations 5.5608284E-02 0.9228001 at 110iterations 3.2645930E-02 0.5451221 at 120iterations 1.9203581E-02 0.3163438 at 130iterations 1.1281242E-02 0.1874437 at 140iterations 6.6462192E-03 0.1103928 at 150iterations 3.9027489E-03 6.7680359E-02 at 160iterations 2.2991898E-03 3.5818100E-02 at 170iterations 1.3503355E-03 2.2445679E-02 at 180iterations finished qdiffx linear iterations at : 12:11:46 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 1.3503355E-03 2.2445679E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.07000 DelPhi exited at 12:11:46 13.070u 0.232s 0:13.63 97.5% 0+0k 0+0io 0pf+0w