Sat Oct 8 16:29:53 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 Sat Oct 8 2011 at 16:29:53 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2457 !!! WARNING: ASP 931 has a net charge of -2.0000 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: 0.6546164 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): -2.834000 45.22400 ymin,ymax (A): -15.96800 28.94000 zmin,zma (A): -17.73600 36.64700 x,y,z range (A): 48.05800 44.90800 54.38300 scale (grids/A): 0.6546164 object centre (A): 21.19500 6.486001 9.455500 number of atom coordinates read : 2457 total number of charged atoms : 2360 net assigned charge : 2.000001 assigned positive charge : 363.0759 centred at (gu) : 90.87608 89.11401 90.60517 assigned negative charge : -361.0768 centred at (gu) : 90.96822 89.32595 90.68063 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7042 nv = 96 ne = 84 npr = 50077 no. pairs analyzed = 50077 no. exposed pairs = 2995 no. arc points = 20961 no. surface atoms = 1016 nbur = 1441 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 426 mr = 3964 m= 2 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3400000 number of dielectric boundary points 3428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2086 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8491 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4352007E-08 -8.9695202E-09 midg,1,midg; midg,igrid,midg 4.5266578E-08 -2.5093655E-08 1,midg,midg; igrid,midg,midg 1.5737509E-08 -1.2807066E-08 gauss-seidel spectral radius is 0.9878938 estimated iterations to convergence 74 setup time was (sec) 0.6200000 now iterating at: 16:29:54 rms-change max change #iterations 0.1522397 23.42033 at 10iterations 1.5768291E-02 2.390839 at 20iterations 1.6614347E-03 0.2567978 at 30iterations 1.8359865E-04 2.5381088E-02 at 40iterations 2.2957092E-05 3.1614304E-03 at 50iterations finished qdiffx linear iterations at : 16:29:57 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 2.2957092E-05 3.1614304E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 16:29:58 4.158u 0.260s 0:04.72 93.4% 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 Sat Oct 8 2011 at 16:29:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2457 !!! WARNING: ASP 931 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.963849 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): -2.834000 45.22400 ymin,ymax (A): -15.96800 28.94000 zmin,zma (A): -17.73600 36.64700 x,y,z range (A): 48.05800 44.90800 54.38300 scale (grids/A): 1.963849 object centre (A): 21.19500 6.486001 9.455500 number of atom coordinates read : 2457 total number of charged atoms : 2360 net assigned charge : 2.000001 assigned positive charge : 363.0759 centred at (gu) : 92.62765 87.34154 91.81496 assigned negative charge : -361.0768 centred at (gu) : 92.90473 87.97769 92.04174 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 75959 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20961 grid for indexing accessible points = 1.400000 m= 28235 mr = 53286 m= 5223 mr = 21203 m= 369 mr = 3654 m= 7 mr = 172 m= 0 mr = 1 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 1215 time to turn everything in is 0.6800000 number of dielectric boundary points 31477 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 18649 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) : 0.6546164 object centre at (A) : 21.19500 6.486001 9.455500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1805516E-02 -1.4480012E-02 midg,1,midg; midg,igrid,midg 2.9792301E-02 -1.5058641E-02 1,midg,midg; igrid,midg,midg 6.8820594E-03 -5.3635389E-02 gauss-seidel spectral radius is 0.9986969 estimated iterations to convergence 219 setup time was (sec) 0.9800000 now iterating at: 16:29:59 rms-change max change #iterations 4.345331 199.2475 at 10iterations 2.062562 74.20400 at 20iterations 0.9827932 41.27986 at 30iterations 0.4689230 15.84405 at 40iterations 0.2233462 7.611458 at 50iterations 0.1066271 3.201004 at 60iterations 5.0737958E-02 1.650991 at 70iterations 2.4166642E-02 0.8149166 at 80iterations 1.1547694E-02 0.3516560 at 90iterations 5.4946365E-03 0.1738033 at 100iterations 2.6295874E-03 8.8590622E-02 at 110iterations 1.2588622E-03 4.5030594E-02 at 120iterations finished qdiffx linear iterations at : 16:30:07 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 1.2588622E-03 4.5030594E-02 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.660000 DelPhi exited at 16:30:08 9.666u 0.332s 0:10.32 96.8% 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 Sat Oct 8 2011 at 16:30:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2457 !!! WARNING: ASP 931 has a net charge of -2.0000 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: 2.945774 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): -2.834000 45.22400 ymin,ymax (A): -15.96800 28.94000 zmin,zma (A): -17.73600 36.64700 x,y,z range (A): 48.05800 44.90800 54.38300 scale (grids/A): 2.945774 object centre (A): 21.19500 6.486001 9.455500 number of atom coordinates read : 2457 total number of charged atoms : 2360 net assigned charge : 2.000001 assigned positive charge : 363.0759 centred at (gu) : 93.94131 86.01212 92.72233 assigned negative charge : -361.0768 centred at (gu) : 94.35705 86.96652 93.06260 start vw surface at 0.1600000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 175868 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20961 grid for indexing accessible points = 1.400000 m= 89711 mr = 129028 m= 34833 mr = 74012 m= 9760 mr = 28857 m= 1575 mr = 7879 m= 138 mr = 1132 m= 3 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 4161 time to turn everything in is 1.770000 number of dielectric boundary points 70910 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 18875 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) : 1.963849 object centre at (A) : 21.19500 6.486001 9.455500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2027839 -0.2515989 midg,1,midg; midg,igrid,midg 0.2261322 -0.1424769 1,midg,midg; igrid,midg,midg 7.7134095E-02 -0.7124251 gauss-seidel spectral radius is 0.9992709 estimated iterations to convergence 292 setup time was (sec) 2.110000 now iterating at: 16:30:10 rms-change max change #iterations 9.998114 466.7034 at 10iterations 5.832435 123.7242 at 20iterations 3.389613 67.67140 at 30iterations 1.968794 39.32814 at 40iterations 1.141174 20.30948 at 50iterations 0.6625901 11.83591 at 60iterations 0.3830799 7.039749 at 70iterations 0.2213919 4.281422 at 80iterations 0.1277823 2.342694 at 90iterations 7.3953144E-02 1.291412 at 100iterations 4.2743698E-02 0.7473469 at 110iterations 2.4644861E-02 0.4786873 at 120iterations 1.4229872E-02 0.2481117 at 130iterations 8.2210759E-03 0.1526222 at 140iterations 4.7387728E-03 8.7223053E-02 at 150iterations 2.7440952E-03 4.5463562E-02 at 160iterations 1.5864577E-03 3.0414581E-02 at 170iterations 9.2014496E-04 1.6420364E-02 at 180iterations finished qdiffx linear iterations at : 16:30:24 total time elapsed so far: 16.10000 # loops : 180 mean,max change (kT/e) : 9.2014496E-04 1.6420364E-02 energy calculations done at 16.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.28000 DelPhi exited at 16:30:25 16.282u 0.310s 0:16.94 97.9% 0+0k 0+0io 0pf+0w