Mon Oct 10 09:45:10 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 09:45:10 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2804 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5826896 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): -20.14100 34.55300 ymin,ymax (A): -60.08800 -4.314000 zmin,zma (A): -0.6970000 60.39900 x,y,z range (A): 54.69400 55.77400 61.09600 scale (grids/A): 0.5826896 object centre (A): 7.205999 -32.20100 29.85100 number of atom coordinates read : 2804 total number of charged atoms : 2653 net assigned charge : 5.014019 assigned positive charge : 412.2549 centred at (gu) : 89.47445 88.59370 87.93534 assigned negative charge : -407.2413 centred at (gu) : 89.58138 88.45504 87.84135 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6582 nv = 96 ne = 84 npr = 53364 no. pairs analyzed = 53364 no. exposed pairs = 4298 no. arc points = 31688 no. surface atoms = 1425 nbur = 1379 mkacc time = 0.1000000 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 = 1.484000 m= 335 mr = 2863 m= 3 mr = 12 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 0.2200000 number of dielectric boundary points 4045 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3052 ## 315 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8114 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3585102E-09 2.0587076E-09 midg,1,midg; midg,igrid,midg -2.5504721E-09 3.0747873E-09 1,midg,midg; igrid,midg,midg 4.0569867E-09 -9.5273078E-10 gauss-seidel spectral radius is 0.9848052 estimated iterations to convergence 67 setup time was (sec) 0.4000000 now iterating at: 09:45:11 rms-change max change #iterations 9.3492761E-02 16.01448 at 10iterations 7.3715448E-03 1.096333 at 20iterations 5.9204025E-04 8.8738441E-02 at 30iterations 6.0128568E-05 9.1495514E-03 at 40iterations 1.0429224E-05 1.2474060E-03 at 50iterations finished qdiffx linear iterations at : 09:45:13 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.0429224E-05 1.2474060E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 09:45:14 3.405u 0.198s 0:03.96 90.6% 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 09:45:14 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2804 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.748069 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): -20.14100 34.55300 ymin,ymax (A): -60.08800 -4.314000 zmin,zma (A): -0.6970000 60.39900 x,y,z range (A): 54.69400 55.77400 61.09600 scale (grids/A): 1.748069 object centre (A): 7.205999 -32.20100 29.85100 number of atom coordinates read : 2804 total number of charged atoms : 2653 net assigned charge : 5.014019 assigned positive charge : 412.2549 centred at (gu) : 88.42295 85.78068 83.80586 assigned negative charge : -407.2413 centred at (gu) : 88.74390 85.36471 83.52372 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31688 grid for indexing accessible points = 1.400000 m= 22379 mr = 41979 m= 3086 mr = 14298 m= 136 mr = 1435 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 37396 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 278 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 20635 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) : 0.5826896 object centre at (A) : 7.205999 -32.20100 29.85100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8850057E-03 7.4313860E-03 midg,1,midg; midg,igrid,midg 1.7308410E-02 2.9415512E-02 1,midg,midg; igrid,midg,midg 1.3191145E-02 1.0564586E-02 gauss-seidel spectral radius is 0.9984345 estimated iterations to convergence 201 setup time was (sec) 0.6000000 now iterating at: 09:45:15 rms-change max change #iterations 3.649547 157.4697 at 10iterations 1.616013 62.40438 at 20iterations 0.7113872 25.99413 at 30iterations 0.3145117 11.28415 at 40iterations 0.1394993 5.570963 at 50iterations 6.1423212E-02 2.273420 at 60iterations 2.7226903E-02 0.9177475 at 70iterations 1.2076412E-02 0.4125707 at 80iterations 5.3469380E-03 0.1970677 at 90iterations 2.3698395E-03 8.4583282E-02 at 100iterations 1.0504420E-03 3.6808729E-02 at 110iterations 4.6551539E-04 1.8083572E-02 at 120iterations finished qdiffx linear iterations at : 09:45:23 total time elapsed so far: 8.450000 # loops : 120 mean,max change (kT/e) : 4.6551539E-04 1.8083572E-02 energy calculations done at 8.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.590000 DelPhi exited at 09:45:23 8.590u 0.251s 0:09.41 93.9% 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 Mon Oct 10 2011 at 09:45:23 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: 273 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2804 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.622103 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): -20.14100 34.55300 ymin,ymax (A): -60.08800 -4.314000 zmin,zma (A): -0.6970000 60.39900 x,y,z range (A): 54.69400 55.77400 61.09600 scale (grids/A): 2.622103 object centre (A): 7.205999 -32.20100 29.85100 number of atom coordinates read : 2804 total number of charged atoms : 2653 net assigned charge : 5.014019 assigned positive charge : 412.2549 centred at (gu) : 87.63421 83.67094 80.70858 assigned negative charge : -407.2413 centred at (gu) : 88.11585 83.04697 80.28563 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 160487 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31688 grid for indexing accessible points = 1.400000 m= 72758 mr = 103678 m= 24429 mr = 54078 m= 5015 mr = 17605 m= 508 mr = 3107 m= 16 mr = 232 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8800000 number of dielectric boundary points 84513 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 21215 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) : 1.748069 object centre at (A) : 7.205999 -32.20100 29.85100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1375985 9.3920469E-02 midg,1,midg; midg,igrid,midg 0.3667515 0.3471128 1,midg,midg; igrid,midg,midg 6.9599412E-02 0.1723828 gauss-seidel spectral radius is 0.9992303 estimated iterations to convergence 285 setup time was (sec) 1.100000 now iterating at: 09:45:25 rms-change max change #iterations 9.432497 357.8215 at 10iterations 5.643978 158.4225 at 20iterations 3.313937 85.52325 at 30iterations 1.928236 51.70674 at 40iterations 1.118321 26.97413 at 50iterations 0.6465034 15.91641 at 60iterations 0.3719477 9.753914 at 70iterations 0.2135741 5.444410 at 80iterations 0.1220990 2.973137 at 90iterations 6.9896571E-02 1.609882 at 100iterations 4.0003933E-02 0.9196076 at 110iterations 2.2844819E-02 0.5976181 at 120iterations 1.3021096E-02 0.2943652 at 130iterations 7.4113985E-03 0.1478739 at 140iterations 4.2255213E-03 8.4291935E-02 at 150iterations 2.3969496E-03 4.8435211E-02 at 160iterations 1.3658354E-03 2.9968262E-02 at 170iterations 7.7760685E-04 1.9650459E-02 at 180iterations finished qdiffx linear iterations at : 09:45:37 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 7.7760685E-04 1.9650459E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.73000 DelPhi exited at 09:45:37 12.735u 0.277s 0:13.98 92.9% 0+0k 0+0io 0pf+0w