Sun Oct 9 16:39:13 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 16:39:13 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 = 2463 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: 0.6366465 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): 8.999001 64.91700 ymin,ymax (A): -17.45400 30.50200 zmin,zma (A): -30.18200 23.18600 x,y,z range (A): 55.91800 47.95600 53.36800 scale (grids/A): 0.6366465 object centre (A): 36.95800 6.524000 -3.498000 number of atom coordinates read : 2463 total number of charged atoms : 2363 net assigned charge : 0.5000063 assigned positive charge : 362.5830 centred at (gu) : 91.64831 90.22581 92.30110 assigned negative charge : -362.0840 centred at (gu) : 91.49117 90.17923 92.16573 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6880 nv = 96 ne = 84 npr = 48791 no. pairs analyzed = 48791 no. exposed pairs = 3249 no. arc points = 23476 no. surface atoms = 1098 nbur = 1365 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 3581 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2900000 number of dielectric boundary points 3634 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2257 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8196 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.1936804E-09 2.1944626E-08 midg,1,midg; midg,igrid,midg -4.3541051E-09 4.8337720E-09 1,midg,midg; igrid,midg,midg -1.0974122E-08 2.1948345E-08 gauss-seidel spectral radius is 0.9872175 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 16:39:14 rms-change max change #iterations 0.1349572 25.71221 at 10iterations 1.3324738E-02 1.869137 at 20iterations 1.3473828E-03 0.2035369 at 30iterations 1.7875158E-04 2.5051117E-02 at 40iterations 3.9901613E-05 5.8908463E-03 at 50iterations finished qdiffx linear iterations at : 16:39:16 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 3.9901613E-05 5.8908463E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 16:39:17 3.367u 0.154s 0:03.81 92.1% 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 16:39:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2463 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: 1.909940 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): 8.999001 64.91700 ymin,ymax (A): -17.45400 30.50200 zmin,zma (A): -30.18200 23.18600 x,y,z range (A): 55.91800 47.95600 53.36800 scale (grids/A): 1.909940 object centre (A): 36.95800 6.524000 -3.498000 number of atom coordinates read : 2463 total number of charged atoms : 2363 net assigned charge : 0.5000063 assigned positive charge : 362.5830 centred at (gu) : 94.94434 90.67676 96.90305 assigned negative charge : -362.0840 centred at (gu) : 94.47340 90.53768 96.49725 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73554 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23476 grid for indexing accessible points = 1.400000 m= 26214 mr = 49119 m= 4250 mr = 18897 m= 294 mr = 2525 m= 3 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1087 time to turn everything in is 0.5500000 number of dielectric boundary points 33656 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 144 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 18597 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) : 0.6366465 object centre at (A) : 36.95800 6.524000 -3.498000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7000949E-02 -2.0995755E-03 midg,1,midg; midg,igrid,midg -6.2500197E-03 8.8980990E-03 1,midg,midg; igrid,midg,midg -1.5597657E-02 1.9903651E-02 gauss-seidel spectral radius is 0.9986429 estimated iterations to convergence 215 setup time was (sec) 0.8500000 now iterating at: 16:39:18 rms-change max change #iterations 4.086936 170.7827 at 10iterations 1.926714 60.21829 at 20iterations 0.9034860 31.67318 at 30iterations 0.4253839 14.59278 at 40iterations 0.2007587 6.697464 at 50iterations 9.4503440E-02 3.398046 at 60iterations 4.4434678E-02 1.614471 at 70iterations 2.0804284E-02 0.7390742 at 80iterations 9.8248785E-03 0.3075562 at 90iterations 4.6170843E-03 0.1536236 at 100iterations 2.1769651E-03 6.5748215E-02 at 110iterations 1.0282366E-03 3.2539368E-02 at 120iterations finished qdiffx linear iterations at : 16:39:25 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 1.0282366E-03 3.2539368E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 16:39:25 7.991u 0.171s 0:08.50 96.0% 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 16:39:25 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 = 2463 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: 2.864909 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): 8.999001 64.91700 ymin,ymax (A): -17.45400 30.50200 zmin,zma (A): -30.18200 23.18600 x,y,z range (A): 55.91800 47.95600 53.36800 scale (grids/A): 2.864909 object centre (A): 36.95800 6.524000 -3.498000 number of atom coordinates read : 2463 total number of charged atoms : 2363 net assigned charge : 0.5000063 assigned positive charge : 362.5830 centred at (gu) : 97.41648 91.01492 100.3545 assigned negative charge : -362.0840 centred at (gu) : 96.71004 90.80644 99.74583 start vw surface at 0.2300000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 170281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23476 grid for indexing accessible points = 1.400000 m= 83950 mr = 119783 m= 30864 mr = 67398 m= 7611 mr = 24525 m= 1209 mr = 5628 m= 114 mr = 770 m= 0 mr = 52 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 3630 time to turn everything in is 1.510000 number of dielectric boundary points 75873 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 18899 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) : 1.909940 object centre at (A) : 36.95800 6.524000 -3.498000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1287449 -8.4615961E-02 midg,1,midg; midg,igrid,midg -7.0798941E-02 0.1004584 1,midg,midg; igrid,midg,midg -0.1391552 7.9009421E-02 gauss-seidel spectral radius is 0.9992723 estimated iterations to convergence 293 setup time was (sec) 1.810000 now iterating at: 16:39:27 rms-change max change #iterations 9.661644 451.2869 at 10iterations 5.714576 155.3531 at 20iterations 3.355012 74.10769 at 30iterations 1.964103 50.48429 at 40iterations 1.145906 21.57389 at 50iterations 0.6660860 12.60424 at 60iterations 0.3871967 8.974023 at 70iterations 0.2245262 4.219456 at 80iterations 0.1301377 2.375690 at 90iterations 7.5416639E-02 1.476471 at 100iterations 4.3657385E-02 0.8022614 at 110iterations 2.5266701E-02 0.5020447 at 120iterations 1.4589590E-02 0.2596231 at 130iterations 8.4307427E-03 0.1561816 at 140iterations 4.8802271E-03 8.8792801E-02 at 150iterations 2.8190957E-03 5.0819397E-02 at 160iterations 1.6334477E-03 3.1782150E-02 at 170iterations 9.4664592E-04 1.8571854E-02 at 180iterations finished qdiffx linear iterations at : 16:39:38 total time elapsed so far: 12.26000 # loops : 180 mean,max change (kT/e) : 9.4664592E-04 1.8571854E-02 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.46000 DelPhi exited at 16:39:38 12.458u 0.184s 0:12.96 97.4% 0+0k 0+0io 0pf+0w