Tue Oct 11 03:15:37 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 Tue Oct 11 2011 at 03:15:37 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3463 !!! WARNING: HIR 410 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5225381 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): 38.01800 94.27700 ymin,ymax (A): 21.15400 72.34500 zmin,zma (A): -9.702000 58.42700 x,y,z range (A): 56.25900 51.19100 68.12900 scale (grids/A): 0.5225381 object centre (A): 66.14750 46.74950 24.36250 number of atom coordinates read : 3463 total number of charged atoms : 3312 net assigned charge : -2.485970 assigned positive charge : 534.4326 centred at (gu) : 89.24743 89.09332 91.09425 assigned negative charge : -536.9208 centred at (gu) : 89.25777 89.06987 91.11840 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6187 nv = 96 ne = 84 npr = 66269 no. pairs analyzed = 66269 no. exposed pairs = 4935 no. arc points = 35161 no. surface atoms = 1620 nbur = 1843 mkacc time = 0.1100000 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 = 1.652000 m= 244 mr = 2824 m= 2 mr = 11 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 0.2400000 number of dielectric boundary points 3598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3500 ## 509 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8253 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3916208E-11 -1.7972220E-10 midg,1,midg; midg,igrid,midg -1.6828616E-10 1.2947149E-11 1,midg,midg; igrid,midg,midg -2.9553752E-11 -7.5189931E-11 gauss-seidel spectral radius is 0.9811874 estimated iterations to convergence 60 setup time was (sec) 0.4200000 now iterating at: 03:15:37 rms-change max change #iterations 6.3479461E-02 10.03350 at 10iterations 3.6585869E-03 0.7318430 at 20iterations 2.1399648E-04 4.3649673E-02 at 30iterations 1.4090587E-05 2.3121834E-03 at 40iterations 1.4243312E-06 2.4986267E-04 at 50iterations finished qdiffx linear iterations at : 03:15:40 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.4243312E-06 2.4986267E-04 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 03:15:41 3.436u 0.167s 0:03.97 90.4% 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 Tue Oct 11 2011 at 03:15:41 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3463 !!! WARNING: HIR 410 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.567614 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): 38.01800 94.27700 ymin,ymax (A): 21.15400 72.34500 zmin,zma (A): -9.702000 58.42700 x,y,z range (A): 56.25900 51.19100 68.12900 scale (grids/A): 1.567614 object centre (A): 66.14750 46.74950 24.36250 number of atom coordinates read : 3463 total number of charged atoms : 3312 net assigned charge : -2.485970 assigned positive charge : 534.4326 centred at (gu) : 87.74122 87.27893 93.28153 assigned negative charge : -536.9208 centred at (gu) : 87.77280 87.20942 93.35464 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68624 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35161 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 19699 mr = 43508 m= 1818 mr = 12352 m= 41 mr = 744 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 33579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 443 ## 9 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 25046 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) : 0.5225381 object centre at (A) : 66.14750 46.74950 24.36250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8922158E-02 -2.4276515E-03 midg,1,midg; midg,igrid,midg -4.9591875E-03 -4.7875806E-03 1,midg,midg; igrid,midg,midg 7.1680034E-03 -2.0900504E-03 gauss-seidel spectral radius is 0.9980991 estimated iterations to convergence 182 setup time was (sec) 0.5400000 now iterating at: 03:15:41 rms-change max change #iterations 3.368930 176.0538 at 10iterations 1.372293 55.29101 at 20iterations 0.5571128 27.18892 at 30iterations 0.2272087 8.448709 at 40iterations 9.2525959E-02 3.266058 at 50iterations 3.7759136E-02 1.408209 at 60iterations 1.5420676E-02 0.5596638 at 70iterations 6.2939152E-03 0.2733688 at 80iterations 2.5702575E-03 0.1008835 at 90iterations 1.0478364E-03 4.2646408E-02 at 100iterations 4.2874666E-04 1.4645576E-02 at 110iterations 1.7404396E-04 6.5221786E-03 at 120iterations finished qdiffx linear iterations at : 03:15:48 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 1.7404396E-04 6.5221786E-03 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 03:15:49 7.663u 0.205s 0:08.17 96.2% 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 Tue Oct 11 2011 at 03:15:49 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3463 !!! WARNING: HIR 410 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.351422 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): 38.01800 94.27700 ymin,ymax (A): 21.15400 72.34500 zmin,zma (A): -9.702000 58.42700 x,y,z range (A): 56.25900 51.19100 68.12900 scale (grids/A): 2.351422 object centre (A): 66.14750 46.74950 24.36250 number of atom coordinates read : 3463 total number of charged atoms : 3312 net assigned charge : -2.485970 assigned positive charge : 534.4326 centred at (gu) : 86.61160 85.91815 94.92216 assigned negative charge : -536.9208 centred at (gu) : 86.65907 85.81396 95.03184 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 159451 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35161 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 68316 mr = 107611 m= 18550 mr = 51138 m= 2606 mr = 12973 m= 130 mr = 1504 m= 0 mr = 32 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8100000 number of dielectric boundary points 75795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 26446 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) : 1.567614 object centre at (A) : 66.14750 46.74950 24.36250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5928021 0.1024972 midg,1,midg; midg,igrid,midg -8.7010704E-02 -7.2819158E-02 1,midg,midg; igrid,midg,midg 0.1104897 -3.6613573E-03 gauss-seidel spectral radius is 0.9991395 estimated iterations to convergence 269 setup time was (sec) 1.050000 now iterating at: 03:15:50 rms-change max change #iterations 9.204720 322.5759 at 10iterations 5.249826 153.2002 at 20iterations 2.961858 69.87211 at 30iterations 1.656572 46.12456 at 40iterations 0.9263857 21.70904 at 50iterations 0.5141890 11.56577 at 60iterations 0.2851732 6.960766 at 70iterations 0.1578490 3.522461 at 80iterations 8.7071255E-02 1.943716 at 90iterations 4.8131429E-02 0.9828434 at 100iterations 2.6542077E-02 0.5821428 at 110iterations 1.4597842E-02 0.3236322 at 120iterations 8.0329692E-03 0.1529665 at 130iterations 4.4261524E-03 9.6861839E-02 at 140iterations 2.4321433E-03 5.9263229E-02 at 150iterations 1.3396405E-03 2.8699875E-02 at 160iterations 7.3543657E-04 1.5035629E-02 at 170iterations 4.0516234E-04 8.5411072E-03 at 180iterations finished qdiffx linear iterations at : 03:16:02 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 4.0516234E-04 8.5411072E-03 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 03:16:02 12.539u 0.202s 0:13.04 97.6% 0+0k 0+0io 0pf+0w