Sun Oct 9 19:11:14 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 Sun Oct 9 2011 at 19:11:14 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4727 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5571205 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): 3.230000 64.59300 ymin,ymax (A): -8.313000 52.37900 zmin,zma (A): -2.263000 61.63700 x,y,z range (A): 61.36300 60.69200 63.90000 scale (grids/A): 0.5571205 object centre (A): 33.91150 22.03300 29.68700 number of atom coordinates read : 4727 total number of charged atoms : 4580 net assigned charge : 2.240029 assigned positive charge : 722.5711 centred at (gu) : 88.16348 89.35173 89.43604 assigned negative charge : -720.3358 centred at (gu) : 88.07246 89.39444 89.39265 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 9831 nv = 96 ne = 84 npr = 93632 no. pairs analyzed = 93632 no. exposed pairs = 5700 no. arc points = 38389 no. surface atoms = 1946 nbur = 2781 mkacc time = 0.2400000 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= 447 mr = 5561 m= 4 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4695 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3991 ## 448 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 12705 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3045646E-10 8.1817364E-10 midg,1,midg; midg,igrid,midg 1.0879666E-09 -3.8107523E-10 1,midg,midg; igrid,midg,midg -1.9711393E-09 1.0840621E-09 gauss-seidel spectral radius is 0.9835178 estimated iterations to convergence 64 setup time was (sec) 0.8200000 now iterating at: 19:11:15 rms-change max change #iterations 0.1101262 15.85519 at 10iterations 1.4865509E-02 1.980530 at 20iterations 6.1555575E-03 0.8318024 at 30iterations 2.9924947E-03 0.4011917 at 40iterations 1.4681553E-03 0.1929092 at 50iterations finished qdiffx linear iterations at : 19:11:20 total time elapsed so far: 5.290000 # loops : 50 mean,max change (kT/e) : 1.4681553E-03 0.1929092 energy calculations done at 5.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.470000 DelPhi exited at 19:11:20 5.472u 0.462s 0:06.22 95.3% 0+0k 0+0io 6pf+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 19:11:20 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4727 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.671361 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): 3.230000 64.59300 ymin,ymax (A): -8.313000 52.37900 zmin,zma (A): -2.263000 61.63700 x,y,z range (A): 61.36300 60.69200 63.90000 scale (grids/A): 1.671361 object centre (A): 33.91150 22.03300 29.68700 number of atom coordinates read : 4727 total number of charged atoms : 4580 net assigned charge : 2.240029 assigned positive charge : 722.5711 centred at (gu) : 84.48875 88.05382 88.30720 assigned negative charge : -720.3358 centred at (gu) : 84.21717 88.18350 88.17770 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 109517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38389 grid for indexing accessible points = 1.400000 m= 39361 mr = 79061 m= 5011 mr = 28649 m= 149 mr = 2669 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9100000 number of dielectric boundary points 43652 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 374 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 35300 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) : 0.5571205 object centre at (A) : 33.91150 22.03300 29.68700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.0721549E-02 -4.7944929E-03 midg,1,midg; midg,igrid,midg 1.6354250E-02 1.0056223E-02 1,midg,midg; igrid,midg,midg -3.4113249E-04 1.5701568E-02 gauss-seidel spectral radius is 0.9984428 estimated iterations to convergence 201 setup time was (sec) 1.300000 now iterating at: 19:11:22 rms-change max change #iterations 4.673256 148.3710 at 10iterations 2.079298 63.51044 at 20iterations 0.9268923 27.81974 at 30iterations 0.4150251 12.95435 at 40iterations 0.1858274 5.856569 at 50iterations 8.4756151E-02 2.432243 at 60iterations 4.0093046E-02 1.534225 at 70iterations 2.0637993E-02 0.6220665 at 80iterations 1.2160962E-02 0.3843231 at 90iterations 8.2448674E-03 0.2621689 at 100iterations 6.0572363E-03 0.1883698 at 110iterations 4.6153432E-03 0.1329575 at 120iterations finished qdiffx linear iterations at : 19:11:34 total time elapsed so far: 13.15000 # loops : 120 mean,max change (kT/e) : 4.6153432E-03 0.1329575 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.32000 DelPhi exited at 19:11:35 13.328u 0.539s 0:14.19 97.6% 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 Sun Oct 9 2011 at 19:11:35 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4727 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.507042 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): 3.230000 64.59300 ymin,ymax (A): -8.313000 52.37900 zmin,zma (A): -2.263000 61.63700 x,y,z range (A): 61.36300 60.69200 63.90000 scale (grids/A): 2.507042 object centre (A): 33.91150 22.03300 29.68700 number of atom coordinates read : 4727 total number of charged atoms : 4580 net assigned charge : 2.240029 assigned positive charge : 722.5711 centred at (gu) : 81.73299 87.08074 87.46026 assigned negative charge : -720.3358 centred at (gu) : 81.32571 87.27532 87.26666 start vw surface at 0.1700000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 254447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38389 grid for indexing accessible points = 1.400000 m= 131221 mr = 192477 m= 42990 mr = 107188 m= 8127 mr = 33536 m= 647 mr = 5576 m= 17 mr = 320 m= 0 mr = 2 time to grow re-entrant surface = 1.520000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.370000 number of dielectric boundary points 98350 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 2.600000 number of grid points assigned charge 36598 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) : 1.671361 object centre at (A) : 33.91150 22.03300 29.68700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3601731 2.2760332E-02 midg,1,midg; midg,igrid,midg 6.6937849E-02 -2.9059131E-02 1,midg,midg; igrid,midg,midg -6.8918772E-02 0.2470779 gauss-seidel spectral radius is 0.9992527 estimated iterations to convergence 289 setup time was (sec) 2.840000 now iterating at: 19:11:38 rms-change max change #iterations 11.85018 341.0518 at 10iterations 6.973567 151.0513 at 20iterations 4.086222 95.75996 at 30iterations 2.377084 45.18598 at 40iterations 1.383849 25.24790 at 50iterations 0.8017401 14.66776 at 60iterations 0.4638312 8.945482 at 70iterations 0.2680535 4.464149 at 80iterations 0.1554462 2.546089 at 90iterations 9.0000838E-02 1.627609 at 100iterations 5.2707829E-02 1.018795 at 110iterations 3.1447195E-02 0.5460358 at 120iterations 1.9422479E-02 0.3372612 at 130iterations 1.2725683E-02 0.2362213 at 140iterations 8.9604091E-03 0.1733932 at 150iterations 6.7806314E-03 0.1272583 at 160iterations 5.4181954E-03 9.5031738E-02 at 170iterations 4.4765989E-03 7.9902649E-02 at 180iterations finished qdiffx linear iterations at : 19:11:59 total time elapsed so far: 23.39000 # loops : 180 mean,max change (kT/e) : 4.4765989E-03 7.9902649E-02 energy calculations done at 23.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.56000 DelPhi exited at 19:11:59 23.567u 0.556s 0:24.41 98.7% 0+0k 0+0io 0pf+0w