Sat Oct 15 14:35:12 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 Sat Oct 15 2011 at 14:35:12 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 = 2824 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6186570 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): -8.828000 48.71600 ymin,ymax (A): -7.772000 39.05400 zmin,zma (A): -0.1980000 57.19400 x,y,z range (A): 57.54400 46.82600 57.39200 scale (grids/A): 0.6186570 object centre (A): 19.94400 15.64100 28.49800 number of atom coordinates read : 2824 total number of charged atoms : 2683 net assigned charge : -0.4999650 assigned positive charge : 423.5343 centred at (gu) : 89.11503 89.66999 88.38558 assigned negative charge : -424.0353 centred at (gu) : 89.00633 89.54881 88.37347 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7342 nv = 96 ne = 84 npr = 55970 no. pairs analyzed = 55970 no. exposed pairs = 3739 no. arc points = 26474 no. surface atoms = 1263 nbur = 1561 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 377 mr = 3807 m= 4 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2200000 number of dielectric boundary points 3884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2671 ## 277 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8920 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5725153E-09 4.0496204E-10 midg,1,midg; midg,igrid,midg -9.4779251E-09 7.4853963E-09 1,midg,midg; igrid,midg,midg -9.6576152E-09 5.9171690E-09 gauss-seidel spectral radius is 0.9864975 estimated iterations to convergence 70 setup time was (sec) 0.4400000 now iterating at: 14:35:14 rms-change max change #iterations 0.1261552 19.04208 at 10iterations 1.1662516E-02 1.921545 at 20iterations 1.0784848E-03 0.1523314 at 30iterations 9.8227021E-05 1.6029358E-02 at 40iterations 1.0696720E-05 1.6555786E-03 at 50iterations finished qdiffx linear iterations at : 14:35:25 total time elapsed so far: 3.790000 # loops : 50 mean,max change (kT/e) : 1.0696720E-05 1.6555786E-03 energy calculations done at 3.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 14:35:26 3.918u 0.272s 0:13.41 31.1% 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 Sat Oct 15 2011 at 14:35:27 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 = 2824 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.855971 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): -8.828000 48.71600 ymin,ymax (A): -7.772000 39.05400 zmin,zma (A): -0.1980000 57.19400 x,y,z range (A): 57.54400 46.82600 57.39200 scale (grids/A): 1.855971 object centre (A): 19.94400 15.64100 28.49800 number of atom coordinates read : 2824 total number of charged atoms : 2683 net assigned charge : -0.4999650 assigned positive charge : 423.5343 centred at (gu) : 87.34445 89.00909 85.15608 assigned negative charge : -424.0353 centred at (gu) : 87.01868 88.64605 85.12018 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 79147 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26474 grid for indexing accessible points = 1.400000 m= 26505 mr = 53185 m= 3780 mr = 18755 m= 167 mr = 2131 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 704 time to turn everything in is 0.4500000 number of dielectric boundary points 35481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 216 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 21032 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) : 0.6186570 object centre at (A) : 19.94400 15.64100 28.49800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6075043E-02 2.2040540E-02 midg,1,midg; midg,igrid,midg -1.8291323E-02 1.2272431E-02 1,midg,midg; igrid,midg,midg -5.3442750E-02 2.7625725E-02 gauss-seidel spectral radius is 0.9985927 estimated iterations to convergence 211 setup time was (sec) 0.7800000 now iterating at: 14:35:29 rms-change max change #iterations 4.219352 186.8464 at 10iterations 1.942766 67.37435 at 20iterations 0.8948707 27.50632 at 30iterations 0.4144242 12.83710 at 40iterations 0.1919699 5.797056 at 50iterations 8.8536896E-02 2.769008 at 60iterations 4.1027971E-02 1.371084 at 70iterations 1.8935455E-02 0.5827637 at 80iterations 8.7577850E-03 0.2663727 at 90iterations 4.0562381E-03 0.1300068 at 100iterations 1.8728939E-03 5.6138039E-02 at 110iterations 8.6770428E-04 2.7420044E-02 at 120iterations finished qdiffx linear iterations at : 14:35:50 total time elapsed so far: 10.01000 # loops : 120 mean,max change (kT/e) : 8.6770428E-04 2.7420044E-02 energy calculations done at 10.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.14000 DelPhi exited at 14:35:51 10.146u 0.332s 0:24.65 42.4% 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 Sat Oct 15 2011 at 14:35:52 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 = 2824 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.783957 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): -8.828000 48.71600 ymin,ymax (A): -7.772000 39.05400 zmin,zma (A): -0.1980000 57.19400 x,y,z range (A): 57.54400 46.82600 57.39200 scale (grids/A): 2.783957 object centre (A): 19.94400 15.64100 28.49800 number of atom coordinates read : 2824 total number of charged atoms : 2683 net assigned charge : -0.4999650 assigned positive charge : 423.5343 centred at (gu) : 86.01650 88.51340 82.73383 assigned negative charge : -424.0353 centred at (gu) : 85.52785 87.96906 82.68020 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 183263 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26474 grid for indexing accessible points = 1.400000 m= 87842 mr = 130002 m= 29664 mr = 69939 m= 6410 mr = 22975 m= 752 mr = 4534 m= 24 mr = 448 m= 0 mr = 4 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 2261 time to turn everything in is 1.110000 number of dielectric boundary points 80053 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 21461 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) : 1.855971 object centre at (A) : 19.94400 15.64100 28.49800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3107584 0.5793900 midg,1,midg; midg,igrid,midg -0.1713454 0.1147053 1,midg,midg; igrid,midg,midg -0.6857874 0.3368751 gauss-seidel spectral radius is 0.9992679 estimated iterations to convergence 292 setup time was (sec) 1.410000 now iterating at: 14:35:56 rms-change max change #iterations 10.22336 315.8314 at 10iterations 6.085803 162.5497 at 20iterations 3.583529 95.47191 at 30iterations 2.094576 50.92198 at 40iterations 1.219645 26.24290 at 50iterations 0.7094489 13.83323 at 60iterations 0.4116695 8.116550 at 70iterations 0.2387991 4.706940 at 80iterations 0.1380690 2.328119 at 90iterations 7.9785563E-02 1.613926 at 100iterations 4.6054088E-02 0.8768263 at 110iterations 2.6584433E-02 0.5621948 at 120iterations 1.5358211E-02 0.3728571 at 130iterations 8.8575995E-03 0.1859262 at 140iterations 5.1101698E-03 9.9035263E-02 at 150iterations 2.9451603E-03 5.4189682E-02 at 160iterations 1.6984361E-03 3.2923698E-02 at 170iterations 9.7991177E-04 1.8247545E-02 at 180iterations finished qdiffx linear iterations at : 14:36:23 total time elapsed so far: 15.61000 # loops : 180 mean,max change (kT/e) : 9.7991177E-04 1.8247545E-02 energy calculations done at 15.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.74000 DelPhi exited at 14:36:24 15.744u 0.319s 0:31.26 51.3% 0+0k 0+0io 0pf+0w