Sun Oct 9 19:14:55 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 19:14:55 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4876 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5576704 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): 2.505000 63.65000 ymin,ymax (A): -7.589000 53.38000 zmin,zma (A): -2.121000 61.71600 x,y,z range (A): 61.14500 60.96900 63.83700 scale (grids/A): 0.5576704 object centre (A): 33.07750 22.89550 29.79750 number of atom coordinates read : 4876 total number of charged atoms : 4748 net assigned charge : 0.6210517 assigned positive charge : 748.4172 centred at (gu) : 88.31963 88.85308 89.33614 assigned negative charge : -747.8016 centred at (gu) : 88.19591 88.86609 89.31455 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9901 nv = 96 ne = 84 npr = 98421 no. pairs analyzed = 98421 no. exposed pairs = 5623 no. arc points = 38659 no. surface atoms = 1936 nbur = 2940 mkacc time = 0.2600000 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= 468 mr = 5711 m= 0 mr = 16 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3991 ## 456 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 13053 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1658798E-10 3.9787065E-10 midg,1,midg; midg,igrid,midg 4.2780715E-10 -9.0868930E-11 1,midg,midg; igrid,midg,midg -3.1077112E-09 1.4457487E-09 gauss-seidel spectral radius is 0.9835550 estimated iterations to convergence 64 setup time was (sec) 0.8800000 now iterating at: 19:14:57 rms-change max change #iterations 0.1101717 14.14828 at 10iterations 1.0244474E-02 1.477425 at 20iterations 3.0043214E-03 0.3442688 at 30iterations 1.3929690E-03 0.1755466 at 40iterations 6.6960789E-04 8.7397575E-02 at 50iterations finished qdiffx linear iterations at : 19:15:02 total time elapsed so far: 5.770000 # loops : 50 mean,max change (kT/e) : 6.6960789E-04 8.7397575E-02 energy calculations done at 5.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.940000 DelPhi exited at 19:15:02 5.947u 0.468s 0:06.71 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 19:15:02 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4876 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.673011 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): 2.505000 63.65000 ymin,ymax (A): -7.589000 53.38000 zmin,zma (A): -2.121000 61.71600 x,y,z range (A): 61.14500 60.96900 63.83700 scale (grids/A): 1.673011 object centre (A): 33.07750 22.89550 29.79750 number of atom coordinates read : 4876 total number of charged atoms : 4748 net assigned charge : 0.6210517 assigned positive charge : 748.4172 centred at (gu) : 84.95745 86.55780 88.00683 assigned negative charge : -747.8016 centred at (gu) : 84.58748 86.59827 87.94328 start vw surface at 0.1800000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 111323 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38659 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 38260 mr = 80936 m= 4607 mr = 27702 m= 146 mr = 2474 m= 1 mr = 26 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 0.9400000 number of dielectric boundary points 43199 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 370 ## 5 charges are in solution ## iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 36592 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) : 0.5576704 object centre at (A) : 33.07750 22.89550 29.79750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9280665E-02 -2.7661385E-02 midg,1,midg; midg,igrid,midg 2.0513784E-02 1.1166993E-02 1,midg,midg; igrid,midg,midg -1.9626433E-03 3.5841193E-02 gauss-seidel spectral radius is 0.9984502 estimated iterations to convergence 202 setup time was (sec) 1.300000 now iterating at: 19:15:04 rms-change max change #iterations 4.787382 192.5716 at 10iterations 2.131158 63.25558 at 20iterations 0.9520690 28.96876 at 30iterations 0.4255451 12.04132 at 40iterations 0.1901346 5.105975 at 50iterations 8.5730128E-02 2.468956 at 60iterations 3.8928866E-02 1.108070 at 70iterations 1.8070346E-02 0.5382681 at 80iterations 8.9564100E-03 0.2575760 at 90iterations 4.9754614E-03 0.1448669 at 100iterations 3.1764121E-03 8.4770203E-02 at 110iterations 2.2354214E-03 5.9677124E-02 at 120iterations finished qdiffx linear iterations at : 19:15:17 total time elapsed so far: 14.02000 # loops : 120 mean,max change (kT/e) : 2.2354214E-03 5.9677124E-02 energy calculations done at 14.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.20000 DelPhi exited at 19:15:17 14.200u 0.541s 0:15.14 97.3% 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 19:15:17 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4876 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.509516 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): 2.505000 63.65000 ymin,ymax (A): -7.589000 53.38000 zmin,zma (A): -2.121000 61.71600 x,y,z range (A): 61.14500 60.96900 63.83700 scale (grids/A): 2.509516 object centre (A): 33.07750 22.89550 29.79750 number of atom coordinates read : 4876 total number of charged atoms : 4748 net assigned charge : 0.6210517 assigned positive charge : 748.4172 centred at (gu) : 82.43575 84.83652 87.00998 assigned negative charge : -747.8016 centred at (gu) : 81.88119 84.89740 86.91498 start vw surface at 0.1600000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 258495 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38659 grid for indexing accessible points = 1.400000 m= 129950 mr = 196261 m= 40961 mr = 106447 m= 7524 mr = 31738 m= 665 mr = 5176 m= 17 mr = 363 m= 0 mr = 0 time to grow re-entrant surface = 1.500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.340000 number of dielectric boundary points 97627 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 2.530000 number of grid points assigned charge 37953 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) : 1.673011 object centre at (A) : 33.07750 22.89550 29.79750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3344335 -0.7341757 midg,1,midg; midg,igrid,midg 0.1128359 6.7945965E-02 1,midg,midg; igrid,midg,midg 4.4872589E-02 0.5816997 gauss-seidel spectral radius is 0.9992555 estimated iterations to convergence 289 setup time was (sec) 2.760000 now iterating at: 19:15:21 rms-change max change #iterations 12.13902 408.4760 at 10iterations 7.178519 213.4114 at 20iterations 4.217015 90.27327 at 30iterations 2.470661 49.53300 at 40iterations 1.434318 28.89613 at 50iterations 0.8337082 13.25009 at 60iterations 0.4826100 8.509171 at 70iterations 0.2791543 4.775112 at 80iterations 0.1614220 2.798565 at 90iterations 9.3088299E-02 1.645771 at 100iterations 5.3932797E-02 0.8452187 at 110iterations 3.1243639E-02 0.5346222 at 120iterations 1.8225253E-02 0.2937088 at 130iterations 1.0807200E-02 0.1855736 at 140iterations 6.5877330E-03 0.1065750 at 150iterations 4.2165243E-03 7.5309753E-02 at 160iterations 2.8889643E-03 5.0312042E-02 at 170iterations 2.1203037E-03 3.6319733E-02 at 180iterations finished qdiffx linear iterations at : 19:15:41 total time elapsed so far: 23.37000 # loops : 180 mean,max change (kT/e) : 2.1203037E-03 3.6319733E-02 energy calculations done at 23.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.53000 DelPhi exited at 19:15:42 23.534u 0.601s 0:24.47 98.6% 0+0k 0+0io 0pf+0w