Tue Oct 11 08:20:59 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 Tue Oct 11 2011 at 08:20:59 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1173 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: 0.7523245 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): -6.923000 31.91900 ymin,ymax (A): 1.065000 39.89000 zmin,zma (A): -1.541000 45.77900 x,y,z range (A): 38.84200 38.82500 47.32000 scale (grids/A): 0.7523245 object centre (A): 12.49800 20.47750 22.11900 number of atom coordinates read : 1173 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 88.75278 89.28739 88.34025 assigned negative charge : -169.8232 centred at (gu) : 88.43077 89.26337 88.36698 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4453 nv = 96 ne = 84 npr = 23117 no. pairs analyzed = 23117 no. exposed pairs = 1520 no. arc points = 11060 no. surface atoms = 517 nbur = 656 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 263 mr = 2274 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 8 time to turn everything in is 0.2500000 number of dielectric boundary points 2407 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 847 ## 68 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 4579 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9863266E-07 8.2720369E-08 midg,1,midg; midg,igrid,midg 1.2734827E-07 1.2794564E-07 1,midg,midg; igrid,midg,midg -1.2828163E-07 2.7315903E-07 gauss-seidel spectral radius is 0.9906932 estimated iterations to convergence 84 setup time was (sec) 0.5200000 now iterating at: 08:21:00 rms-change max change #iterations 0.1900315 40.17935 at 10iterations 2.5930952E-02 4.942262 at 20iterations 3.4616056E-03 0.5666351 at 30iterations 4.7440789E-04 7.5232506E-02 at 40iterations 6.6425346E-05 1.0768890E-02 at 50iterations finished qdiffx linear iterations at : 08:21:03 total time elapsed so far: 3.700000 # loops : 50 mean,max change (kT/e) : 6.6425346E-05 1.0768890E-02 energy calculations done at 3.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.930000 DelPhi exited at 08:21:04 3.934u 0.163s 0:04.75 86.1% 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 Tue Oct 11 2011 at 08:21:04 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1173 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: 2.256974 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): -6.923000 31.91900 ymin,ymax (A): 1.065000 39.89000 zmin,zma (A): -1.541000 45.77900 x,y,z range (A): 38.84200 38.82500 47.32000 scale (grids/A): 2.256974 object centre (A): 12.49800 20.47750 22.11900 number of atom coordinates read : 1173 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 86.25833 87.86240 85.02090 assigned negative charge : -169.8232 centred at (gu) : 85.29245 87.79037 85.10107 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 46468 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11060 grid for indexing accessible points = 1.400000 m= 17038 mr = 30176 m= 3187 mr = 12566 m= 291 mr = 2131 m= 16 mr = 137 m= 0 mr = 2 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 194 time to turn everything in is 0.4800000 number of dielectric boundary points 21988 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 8452 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) : 0.7523245 object centre at (A) : 12.49800 20.47750 22.11900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9606083E-02 4.5237271E-03 midg,1,midg; midg,igrid,midg 4.0506911E-02 3.3334013E-02 1,midg,midg; igrid,midg,midg -3.3097759E-02 4.7026388E-02 gauss-seidel spectral radius is 0.9988633 estimated iterations to convergence 235 setup time was (sec) 0.8400000 now iterating at: 08:21:05 rms-change max change #iterations 3.720581 227.7402 at 10iterations 1.847186 74.14285 at 20iterations 0.9246365 36.63012 at 30iterations 0.4617473 18.50371 at 40iterations 0.2304997 8.294775 at 50iterations 0.1153975 4.968750 at 60iterations 5.7258792E-02 2.159409 at 70iterations 2.8710667E-02 1.072208 at 80iterations 1.4341254E-02 0.5515633 at 90iterations 7.1479240E-03 0.2752609 at 100iterations 3.5660828E-03 0.1292448 at 110iterations 1.7916994E-03 6.6045761E-02 at 120iterations finished qdiffx linear iterations at : 08:21:13 total time elapsed so far: 9.170000 # loops : 120 mean,max change (kT/e) : 1.7916994E-03 6.6045761E-02 energy calculations done at 9.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.400000 DelPhi exited at 08:21:14 9.402u 0.313s 0:10.05 96.6% 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 Tue Oct 11 2011 at 08:21:14 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1173 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: 3.385460 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): -6.923000 31.91900 ymin,ymax (A): 1.065000 39.89000 zmin,zma (A): -1.541000 45.77900 x,y,z range (A): 38.84200 38.82500 47.32000 scale (grids/A): 3.385460 object centre (A): 12.49800 20.47750 22.11900 number of atom coordinates read : 1173 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 84.38754 86.79357 82.53135 assigned negative charge : -169.8232 centred at (gu) : 82.93873 86.68557 82.65166 start vw surface at 0.1500000 fill in re-entrant regions at 0.7200000 boundary points on vw surface= 106845 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11060 grid for indexing accessible points = 1.400000 m= 53038 mr = 72912 m= 21426 mr = 42977 m= 6028 mr = 17504 m= 1171 mr = 4673 m= 160 mr = 844 m= 5 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 531 time to turn everything in is 1.500000 number of dielectric boundary points 49678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 8488 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) : 2.256974 object centre at (A) : 12.49800 20.47750 22.11900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3494137 4.8405450E-02 midg,1,midg; midg,igrid,midg 0.3375679 0.2748109 1,midg,midg; igrid,midg,midg -0.2667485 0.3348846 gauss-seidel spectral radius is 0.9992992 estimated iterations to convergence 298 setup time was (sec) 1.900000 now iterating at: 08:21:16 rms-change max change #iterations 8.046335 292.6280 at 10iterations 4.692431 111.5441 at 20iterations 2.726901 65.15853 at 30iterations 1.588363 38.82805 at 40iterations 0.9249465 18.35111 at 50iterations 0.5376583 11.71125 at 60iterations 0.3120879 6.863091 at 70iterations 0.1815288 3.816230 at 80iterations 0.1056678 2.213552 at 90iterations 6.1455239E-02 1.336584 at 100iterations 3.5782482E-02 0.7918739 at 110iterations 2.0736992E-02 0.4158945 at 120iterations 1.2042046E-02 0.2620239 at 130iterations 7.0137084E-03 0.1466398 at 140iterations 4.0817754E-03 8.5716486E-02 at 150iterations 2.3734223E-03 5.0670624E-02 at 160iterations 1.3806404E-03 2.9556274E-02 at 170iterations 8.0443092E-04 1.9279480E-02 at 180iterations finished qdiffx linear iterations at : 08:21:30 total time elapsed so far: 15.18000 # loops : 180 mean,max change (kT/e) : 8.0443092E-04 1.9279480E-02 energy calculations done at 15.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.43000 DelPhi exited at 08:21:31 15.436u 0.338s 0:16.43 95.9% 0+0k 0+0io 0pf+0w