Sun Oct 9 10:34:34 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 Sun Oct 9 2011 at 10:34:34 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2905 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: HIR 212 has a net charge of 0.5140 !!! WARNING: CME 218 has a net charge of -0.3480 !!! WARNING: CME 313 has a net charge of -0.3480 !!! WARNING: CME 462 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 0.5828040 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): -21.85400 39.23000 ymin,ymax (A): -25.38500 29.78200 zmin,zma (A): -29.72500 26.69800 x,y,z range (A): 61.08400 55.16700 56.42300 scale (grids/A): 0.5828040 object centre (A): 8.688002 2.198500 -1.513500 number of atom coordinates read : 2905 total number of charged atoms : 2810 net assigned charge : 0.4470257 assigned positive charge : 433.0409 centred at (gu) : 89.61426 89.88626 91.52857 assigned negative charge : -432.5957 centred at (gu) : 89.57543 89.82991 91.45620 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6865 nv = 96 ne = 84 npr = 56023 no. pairs analyzed = 56023 no. exposed pairs = 4084 no. arc points = 28258 no. surface atoms = 1346 nbur = 1559 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 = 1.484000 m= 339 mr = 3452 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3730 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2840 ## 294 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8576 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1342494E-09 2.5464795E-09 midg,1,midg; midg,igrid,midg -1.2799649E-09 1.3603683E-09 1,midg,midg; igrid,midg,midg -9.1041247E-10 9.0498781E-10 gauss-seidel spectral radius is 0.9848108 estimated iterations to convergence 67 setup time was (sec) 0.6600000 now iterating at: 10:34:35 rms-change max change #iterations 9.9530824E-02 18.06991 at 10iterations 8.2863215E-03 1.449104 at 20iterations 9.8867342E-04 0.1569633 at 30iterations 2.3042999E-04 3.9401531E-02 at 40iterations 6.7688125E-05 1.1525631E-02 at 50iterations finished qdiffx linear iterations at : 10:34:38 total time elapsed so far: 4.160000 # loops : 50 mean,max change (kT/e) : 6.7688125E-05 1.1525631E-02 energy calculations done at 4.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 10:34:39 4.354u 0.293s 0:05.04 92.0% 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 Sun Oct 9 2011 at 10:34:39 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2905 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: HIR 212 has a net charge of 0.5140 !!! WARNING: CME 218 has a net charge of -0.3480 !!! WARNING: CME 313 has a net charge of -0.3480 !!! WARNING: CME 462 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 1.748412 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): -21.85400 39.23000 ymin,ymax (A): -25.38500 29.78200 zmin,zma (A): -29.72500 26.69800 x,y,z range (A): 61.08400 55.16700 56.42300 scale (grids/A): 1.748412 object centre (A): 8.688002 2.198500 -1.513500 number of atom coordinates read : 2905 total number of charged atoms : 2810 net assigned charge : 0.4470257 assigned positive charge : 433.0409 centred at (gu) : 88.84177 89.65773 94.58461 assigned negative charge : -432.5957 centred at (gu) : 88.72635 89.48988 94.36885 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 75299 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28258 grid for indexing accessible points = 1.400000 m= 24537 mr = 50529 m= 3240 mr = 16353 m= 156 mr = 1674 m= 3 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 535 time to turn everything in is 0.6600000 number of dielectric boundary points 34654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 239 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 21907 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) : 0.5828040 object centre at (A) : 8.688002 2.198500 -1.513500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7025373E-03 1.6413530E-02 midg,1,midg; midg,igrid,midg 3.4118912E-03 1.0838351E-02 1,midg,midg; igrid,midg,midg -4.8562652E-03 -1.1099568E-02 gauss-seidel spectral radius is 0.9984405 estimated iterations to convergence 201 setup time was (sec) 1.010000 now iterating at: 10:34:40 rms-change max change #iterations 3.781244 160.7146 at 10iterations 1.659784 66.21197 at 20iterations 0.7398000 28.53107 at 30iterations 0.3269672 10.35752 at 40iterations 0.1451164 5.249142 at 50iterations 6.4499997E-02 2.016943 at 60iterations 2.8692409E-02 1.055115 at 70iterations 1.2823606E-02 0.4303455 at 80iterations 5.7750768E-03 0.1944084 at 90iterations 2.6296494E-03 9.6280098E-02 at 100iterations 1.2203484E-03 4.3965340E-02 at 110iterations 5.9441006E-04 2.4822235E-02 at 120iterations finished qdiffx linear iterations at : 10:34:49 total time elapsed so far: 9.940000 # loops : 120 mean,max change (kT/e) : 5.9441006E-04 2.4822235E-02 energy calculations done at 9.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.12000 DelPhi exited at 10:34:49 10.121u 0.306s 0:10.79 96.5% 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 Sun Oct 9 2011 at 10:34:50 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2905 !!! WARNING: CME 113 has a net charge of -0.3480 !!! WARNING: HIR 212 has a net charge of 0.5140 !!! WARNING: CME 218 has a net charge of -0.3480 !!! WARNING: CME 313 has a net charge of -0.3480 !!! WARNING: CME 462 has a net charge of -0.3480 !!! WARNING: CME 1 has a net charge of -0.0350 !!! WARNING: CME 3 has a net charge of -0.0350 !!! WARNING: CME 5 has a net charge of -0.0350 !!! WARNING: CME 7 has a net charge of -0.0350 !!! WARNING: CME 9 has a net charge of -0.0350 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: 2.622618 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): -21.85400 39.23000 ymin,ymax (A): -25.38500 29.78200 zmin,zma (A): -29.72500 26.69800 x,y,z range (A): 61.08400 55.16700 56.42300 scale (grids/A): 2.622618 object centre (A): 8.688002 2.198500 -1.513500 number of atom coordinates read : 2905 total number of charged atoms : 2810 net assigned charge : 0.4470257 assigned positive charge : 433.0409 centred at (gu) : 88.26242 89.48644 96.87680 assigned negative charge : -432.5957 centred at (gu) : 88.08944 89.23492 96.55328 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 174141 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28258 grid for indexing accessible points = 1.400000 m= 81984 mr = 123590 m= 26419 mr = 63592 m= 5584 mr = 19381 m= 589 mr = 3741 m= 13 mr = 300 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 1842 time to turn everything in is 1.420000 number of dielectric boundary points 78126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 22473 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) : 1.748412 object centre at (A) : 8.688002 2.198500 -1.513500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.2411351E-02 0.2240432 midg,1,midg; midg,igrid,midg 0.1810079 0.1481968 1,midg,midg; igrid,midg,midg -1.1224420E-03 -0.2272757 gauss-seidel spectral radius is 0.9992202 estimated iterations to convergence 283 setup time was (sec) 1.770000 now iterating at: 10:34:52 rms-change max change #iterations 9.575919 279.0519 at 10iterations 5.612602 156.5691 at 20iterations 3.255884 71.86916 at 30iterations 1.880030 40.54174 at 40iterations 1.082386 20.55674 at 50iterations 0.6195229 12.11372 at 60iterations 0.3543370 7.990524 at 70iterations 0.2020215 4.017914 at 80iterations 0.1150938 2.437225 at 90iterations 6.5483145E-02 1.301228 at 100iterations 3.7301168E-02 0.6958790 at 110iterations 2.1176411E-02 0.3853526 at 120iterations 1.2075182E-02 0.2452183 at 130iterations 6.8892622E-03 0.1343584 at 140iterations 3.9394344E-03 7.5191498E-02 at 150iterations 2.2736746E-03 4.3334961E-02 at 160iterations 1.3272220E-03 2.6813507E-02 at 170iterations 7.9143757E-04 1.5792847E-02 at 180iterations finished qdiffx linear iterations at : 10:35:06 total time elapsed so far: 16.12000 # loops : 180 mean,max change (kT/e) : 7.9143757E-04 1.5792847E-02 energy calculations done at 16.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.30000 DelPhi exited at 10:35:06 16.304u 0.271s 0:16.93 97.8% 0+0k 0+0io 0pf+0w