Sat Oct 8 11:37:36 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 11:37:36 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 = 3114 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: 0.5580550 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): 0.1220000 60.04400 ymin,ymax (A): -18.85700 32.94600 zmin,zma (A): -7.530000 56.26300 x,y,z range (A): 59.92200 51.80300 63.79300 scale (grids/A): 0.5580550 object centre (A): 30.08300 7.044499 24.36650 number of atom coordinates read : 3114 total number of charged atoms : 2954 net assigned charge : -6.499985 assigned positive charge : 454.9947 centred at (gu) : 91.26365 88.40212 88.36400 assigned negative charge : -461.4961 centred at (gu) : 91.23470 88.34721 88.26395 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6819 nv = 96 ne = 84 npr = 58617 no. pairs analyzed = 58617 no. exposed pairs = 4524 no. arc points = 33515 no. surface atoms = 1521 nbur = 1593 mkacc time = 0.1600000 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 = 1.540000 m= 322 mr = 3147 m= 0 mr = 11 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3304 ## 393 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8496 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.5208584E-09 2.8686520E-10 midg,1,midg; midg,igrid,midg -1.7682100E-09 -2.9072200E-11 1,midg,midg; igrid,midg,midg -6.8210482E-10 -4.0391662E-10 gauss-seidel spectral radius is 0.9834748 estimated iterations to convergence 64 setup time was (sec) 0.6300000 now iterating at: 11:37:37 rms-change max change #iterations 8.3468556E-02 15.95829 at 10iterations 5.7829795E-03 0.9769363 at 20iterations 4.0723052E-04 6.5237045E-02 at 30iterations 2.9005736E-05 4.8923492E-03 at 40iterations 2.0579305E-06 3.7384033E-04 at 50iterations finished qdiffx linear iterations at : 11:37:41 total time elapsed so far: 4.560000 # loops : 50 mean,max change (kT/e) : 2.0579305E-06 3.7384033E-04 energy calculations done at 4.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.730000 DelPhi exited at 11:37:42 4.737u 0.410s 0:05.63 91.2% 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 Sat Oct 8 2011 at 11:37:42 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 = 3114 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: 1.674165 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): 0.1220000 60.04400 ymin,ymax (A): -18.85700 32.94600 zmin,zma (A): -7.530000 56.26300 x,y,z range (A): 59.92200 51.80300 63.79300 scale (grids/A): 1.674165 object centre (A): 30.08300 7.044499 24.36650 number of atom coordinates read : 3114 total number of charged atoms : 2954 net assigned charge : -6.499985 assigned positive charge : 454.9947 centred at (gu) : 93.79000 85.20534 85.09132 assigned negative charge : -461.4961 centred at (gu) : 93.70377 85.04149 84.79144 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 74057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33515 grid for indexing accessible points = 1.400000 m= 23442 mr = 46716 m= 2738 mr = 15441 m= 89 mr = 1297 m= 3 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 36861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 358 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 22788 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) : 0.5580550 object centre at (A) : 30.08300 7.044499 24.36650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2319633E-02 -4.9191341E-03 midg,1,midg; midg,igrid,midg -1.1505850E-02 -2.5337229E-03 1,midg,midg; igrid,midg,midg -1.0974609E-02 -1.2367779E-02 gauss-seidel spectral radius is 0.9983172 estimated iterations to convergence 194 setup time was (sec) 0.9200000 now iterating at: 11:37:43 rms-change max change #iterations 3.588945 155.4370 at 10iterations 1.532982 58.08753 at 20iterations 0.6610489 22.17943 at 30iterations 0.2830706 10.64480 at 40iterations 0.1214625 4.476611 at 50iterations 5.2276418E-02 1.830115 at 60iterations 2.2439834E-02 0.7707005 at 70iterations 9.6208099E-03 0.4257145 at 80iterations 4.1484460E-03 0.1410246 at 90iterations 1.7884700E-03 6.2731981E-02 at 100iterations 7.6882256E-04 2.7902603E-02 at 110iterations 3.3086757E-04 1.3370514E-02 at 120iterations finished qdiffx linear iterations at : 11:37:53 total time elapsed so far: 10.73000 # loops : 120 mean,max change (kT/e) : 3.3086757E-04 1.3370514E-02 energy calculations done at 10.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.89000 DelPhi exited at 11:37:53 10.899u 0.468s 0:11.71 96.9% 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 Sat Oct 8 2011 at 11:37:53 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 = 3114 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: 2.511247 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): 0.1220000 60.04400 ymin,ymax (A): -18.85700 32.94600 zmin,zma (A): -7.530000 56.26300 x,y,z range (A): 59.92200 51.80300 63.79300 scale (grids/A): 2.511247 object centre (A): 30.08300 7.044499 24.36650 number of atom coordinates read : 3114 total number of charged atoms : 2954 net assigned charge : -6.499985 assigned positive charge : 454.9947 centred at (gu) : 95.68468 82.80762 82.63663 assigned negative charge : -461.4961 centred at (gu) : 95.55569 82.56222 82.18708 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 171552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33515 grid for indexing accessible points = 1.400000 m= 77960 mr = 115190 m= 24359 mr = 59471 m= 4349 mr = 17959 m= 373 mr = 2769 m= 19 mr = 174 m= 0 mr = 4 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.530000 number of dielectric boundary points 83045 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 23616 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) : 1.674165 object centre at (A) : 30.08300 7.044499 24.36650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9083775 4.5983066E-04 midg,1,midg; midg,igrid,midg -0.1566730 -3.4545440E-02 1,midg,midg; igrid,midg,midg -0.1486651 -0.2043694 gauss-seidel spectral radius is 0.9991981 estimated iterations to convergence 279 setup time was (sec) 1.890000 now iterating at: 11:37:56 rms-change max change #iterations 9.256739 308.0287 at 10iterations 5.330215 131.3223 at 20iterations 3.051169 64.92004 at 30iterations 1.743090 35.36922 at 40iterations 0.9873583 19.80063 at 50iterations 0.5571528 12.14767 at 60iterations 0.3151519 6.348461 at 70iterations 0.1779343 3.325205 at 80iterations 0.1000618 1.903564 at 90iterations 5.6333233E-02 1.252769 at 100iterations 3.1607606E-02 0.6193962 at 110iterations 1.7743528E-02 0.3639424 at 120iterations 9.9830879E-03 0.2046795 at 130iterations 5.5972673E-03 0.1076660 at 140iterations 3.1395161E-03 5.8609009E-02 at 150iterations 1.7649370E-03 3.6998749E-02 at 160iterations 9.8973303E-04 1.8960953E-02 at 170iterations 5.5565435E-04 1.3023376E-02 at 180iterations finished qdiffx linear iterations at : 11:38:13 total time elapsed so far: 19.20000 # loops : 180 mean,max change (kT/e) : 5.5565435E-04 1.3023376E-02 energy calculations done at 19.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.38000 DelPhi exited at 11:38:14 19.384u 0.475s 0:20.22 98.1% 0+0k 0+0io 0pf+0w