Mon Oct 10 10:19:07 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 Mon Oct 10 2011 at 10:19:07 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2862 !!! WARNING: HIT 235 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5395411 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): -21.83600 44.14600 ymin,ymax (A): 31.84700 86.50900 zmin,zma (A): 26.89100 79.23100 x,y,z range (A): 65.98200 54.66200 52.34000 scale (grids/A): 0.5395411 object centre (A): 11.15500 59.17800 53.06100 number of atom coordinates read : 2862 total number of charged atoms : 2710 net assigned charge : 6.014013 assigned positive charge : 418.1409 centred at (gu) : 91.64575 89.56702 92.97444 assigned negative charge : -412.1273 centred at (gu) : 91.79444 89.52715 93.08375 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5531 nv = 96 ne = 84 npr = 55435 no. pairs analyzed = 55435 no. exposed pairs = 4322 no. arc points = 31540 no. surface atoms = 1437 nbur = 1425 mkacc time = 0.1400000 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 = 1.596000 m= 242 mr = 2384 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3101 ## 414 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7261 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9925971E-10 -4.7183729E-10 midg,1,midg; midg,igrid,midg 1.4123271E-10 4.5491799E-10 1,midg,midg; igrid,midg,midg 6.7131645E-10 -6.2098432E-10 gauss-seidel spectral radius is 0.9823015 estimated iterations to convergence 62 setup time was (sec) 0.5600000 now iterating at: 10:19:08 rms-change max change #iterations 6.7923151E-02 13.62309 at 10iterations 4.3534003E-03 0.8052263 at 20iterations 3.0001823E-04 5.8364868E-02 at 30iterations 2.9757965E-05 4.6014786E-03 at 40iterations 4.9999394E-06 6.8569183E-04 at 50iterations finished qdiffx linear iterations at : 10:19:11 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 4.9999394E-06 6.8569183E-04 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 10:19:11 3.466u 0.174s 0:03.97 91.4% 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 10:19:11 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2862 !!! WARNING: HIT 235 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.618623 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): -21.83600 44.14600 ymin,ymax (A): 31.84700 86.50900 zmin,zma (A): 26.89100 79.23100 x,y,z range (A): 65.98200 54.66200 52.34000 scale (grids/A): 1.618623 object centre (A): 11.15500 59.17800 53.06100 number of atom coordinates read : 2862 total number of charged atoms : 2710 net assigned charge : 6.014013 assigned positive charge : 418.1409 centred at (gu) : 94.93656 88.70052 98.92284 assigned negative charge : -412.1273 centred at (gu) : 95.38303 88.58109 99.25081 start vw surface at 0.1800000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 60216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31540 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18024 mr = 36404 m= 1899 mr = 11350 m= 60 mr = 717 m= 2 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 31729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 345 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 20694 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) : 0.5395411 object centre at (A) : 11.15500 59.17800 53.06100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9255917E-03 -7.7621709E-04 midg,1,midg; midg,igrid,midg -2.9300353E-03 1.3374071E-02 1,midg,midg; igrid,midg,midg 1.2657531E-02 -1.3715560E-02 gauss-seidel spectral radius is 0.9981551 estimated iterations to convergence 185 setup time was (sec) 0.8900000 now iterating at: 10:19:12 rms-change max change #iterations 3.108490 182.0035 at 10iterations 1.281925 50.65028 at 20iterations 0.5298067 19.62822 at 30iterations 0.2181751 7.980843 at 40iterations 8.9927427E-02 3.569187 at 50iterations 3.7262190E-02 1.341785 at 60iterations 1.5355994E-02 0.5620079 at 70iterations 6.3432599E-03 0.2500591 at 80iterations 2.6225459E-03 0.1051483 at 90iterations 1.0858205E-03 4.2339325E-02 at 100iterations 4.5080381E-04 1.8726349E-02 at 110iterations 1.8851466E-04 7.2166920E-03 at 120iterations finished qdiffx linear iterations at : 10:19:20 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 1.8851466E-04 7.2166920E-03 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.250000 DelPhi exited at 10:19:20 8.248u 0.290s 0:08.83 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 Mon Oct 10 2011 at 10:19:20 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2862 !!! WARNING: HIT 235 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.427935 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): -21.83600 44.14600 ymin,ymax (A): 31.84700 86.50900 zmin,zma (A): 26.89100 79.23100 x,y,z range (A): 65.98200 54.66200 52.34000 scale (grids/A): 2.427935 object centre (A): 11.15500 59.17800 53.06100 number of atom coordinates read : 2862 total number of charged atoms : 2710 net assigned charge : 6.014013 assigned positive charge : 418.1409 centred at (gu) : 97.40484 88.05079 103.3841 assigned negative charge : -412.1273 centred at (gu) : 98.07446 87.87150 103.8762 start vw surface at 0.1900000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 139485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31540 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 61140 mr = 90463 m= 17651 mr = 45371 m= 2698 mr = 12243 m= 155 mr = 1483 m= 10 mr = 44 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 71536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 21649 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) : 1.618623 object centre at (A) : 11.15500 59.17800 53.06100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4743210E-02 2.2074575E-02 midg,1,midg; midg,igrid,midg -0.1579875 0.2587062 1,midg,midg; igrid,midg,midg 0.3266906 -0.5329592 gauss-seidel spectral radius is 0.9991367 estimated iterations to convergence 269 setup time was (sec) 1.560000 now iterating at: 10:19:22 rms-change max change #iterations 8.348083 281.9463 at 10iterations 4.764021 143.4337 at 20iterations 2.687021 97.00233 at 30iterations 1.511380 40.42308 at 40iterations 0.8423598 23.40473 at 50iterations 0.4686090 11.85143 at 60iterations 0.2595472 6.410648 at 70iterations 0.1435907 3.576541 at 80iterations 7.9229996E-02 2.011663 at 90iterations 4.3764472E-02 1.092888 at 100iterations 2.4050675E-02 0.7058926 at 110iterations 1.3293608E-02 0.3000910 at 120iterations 7.3085739E-03 0.1735644 at 130iterations 4.0079351E-03 8.5161209E-02 at 140iterations 2.2017828E-03 5.3261280E-02 at 150iterations 1.2113868E-03 2.8404236E-02 at 160iterations 6.6566630E-04 1.4228344E-02 at 170iterations 3.6593759E-04 8.9988708E-03 at 180iterations finished qdiffx linear iterations at : 10:19:32 total time elapsed so far: 12.00000 # loops : 180 mean,max change (kT/e) : 3.6593759E-04 8.9988708E-03 energy calculations done at 12.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 10:19:33 12.195u 0.187s 0:12.69 97.4% 0+0k 0+0io 0pf+0w