Mon Oct 10 12:14:30 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 Mon Oct 10 2011 at 12:14:30 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7511182 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): -23.10600 23.96200 ymin,ymax (A): -7.368000 35.77300 zmin,zma (A): -3.355000 44.04100 x,y,z range (A): 47.06800 43.14100 47.39600 scale (grids/A): 0.7511182 object centre (A): 0.4280005 14.20250 20.34300 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 89.69821 90.39363 90.27534 assigned negative charge : -323.3720 centred at (gu) : 89.72850 90.49218 90.46780 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8300 nv = 96 ne = 84 npr = 43706 no. pairs analyzed = 43706 no. exposed pairs = 2739 no. arc points = 19374 no. surface atoms = 932 nbur = 1185 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 674 mr = 4639 m= 7 mr = 155 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.2800000 number of dielectric boundary points 4187 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1529 ## 103 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8630 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.8200751E-08 -4.1068105E-07 midg,1,midg; midg,igrid,midg -1.2992227E-08 -2.8629711E-07 1,midg,midg; igrid,midg,midg -1.0524393E-07 -1.6825088E-07 gauss-seidel spectral radius is 0.9907644 estimated iterations to convergence 85 setup time was (sec) 0.5400000 now iterating at: 12:15:34 rms-change max change #iterations 0.2647645 39.55509 at 10iterations 3.6801394E-02 4.774714 at 20iterations 5.0762217E-03 0.7319965 at 30iterations 7.1442232E-04 8.0863953E-02 at 40iterations 9.7826305E-05 1.2227297E-02 at 50iterations finished qdiffx linear iterations at : 12:15:38 total time elapsed so far: 4.700000 # loops : 50 mean,max change (kT/e) : 9.7826305E-05 1.2227297E-02 energy calculations done at 4.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.860000 DelPhi exited at 12:15:38 4.860u 0.622s 1:07.77 8.0% 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 Mon Oct 10 2011 at 12:15:38 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.253355 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): -23.10600 23.96200 ymin,ymax (A): -7.368000 35.77300 zmin,zma (A): -3.355000 44.04100 x,y,z range (A): 47.06800 43.14100 47.39600 scale (grids/A): 2.253355 object centre (A): 0.4280005 14.20250 20.34300 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 89.09461 91.18096 90.82598 assigned negative charge : -323.3720 centred at (gu) : 89.18566 91.47662 91.40337 start vw surface at 0.1000000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 86292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19374 grid for indexing accessible points = 1.400000 m= 36484 mr = 59365 m= 8973 mr = 28010 m= 1165 mr = 6424 m= 40 mr = 661 m= 0 mr = 3 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 798 time to turn everything in is 0.7300000 number of dielectric boundary points 38491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 15769 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) : 0.7511182 object centre at (A) : 0.4280005 14.20250 20.34300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8722907E-03 -0.1494814 midg,1,midg; midg,igrid,midg -1.9951250E-02 -3.9361287E-02 1,midg,midg; igrid,midg,midg -1.3138503E-02 -2.5928261E-02 gauss-seidel spectral radius is 0.9989548 estimated iterations to convergence 245 setup time was (sec) 1.130000 now iterating at: 12:15:40 rms-change max change #iterations 5.212184 227.4979 at 10iterations 2.666764 90.99751 at 20iterations 1.369666 41.85826 at 30iterations 0.7032990 19.51172 at 40iterations 0.3637758 9.533680 at 50iterations 0.1867206 5.214226 at 60iterations 9.5803142E-02 2.785869 at 70iterations 4.9504679E-02 1.353882 at 80iterations 2.5338912E-02 0.6760159 at 90iterations 1.3033007E-02 0.3537827 at 100iterations 6.7248400E-03 0.1861420 at 110iterations 3.4594999E-03 9.5771790E-02 at 120iterations finished qdiffx linear iterations at : 12:15:50 total time elapsed so far: 11.36000 # loops : 120 mean,max change (kT/e) : 3.4594999E-03 9.5771790E-02 energy calculations done at 11.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.53000 DelPhi exited at 12:15:51 11.538u 0.497s 0:12.48 96.3% 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 Mon Oct 10 2011 at 12:15:51 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.380032 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): -23.10600 23.96200 ymin,ymax (A): -7.368000 35.77300 zmin,zma (A): -3.355000 44.04100 x,y,z range (A): 47.06800 43.14100 47.39600 scale (grids/A): 3.380032 object centre (A): 0.4280005 14.20250 20.34300 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.0999 centred at (gu) : 88.64186 91.77148 91.23888 assigned negative charge : -323.3720 centred at (gu) : 88.77838 92.21494 92.10503 start vw surface at 0.1000000 fill in re-entrant regions at 0.9000000 boundary points on vw surface= 198222 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19374 grid for indexing accessible points = 1.400000 m= 109000 mr = 142778 m= 50316 mr = 90379 m= 17507 mr = 42290 m= 4559 mr = 14124 m= 799 mr = 3505 m= 46 mr = 555 m= 0 mr = 12 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 2679 time to turn everything in is 2.340000 number of dielectric boundary points 86806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.490000 number of grid points assigned charge 15824 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) : 2.253355 object centre at (A) : 0.4280005 14.20250 20.34300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0531923E-02 -1.285986 midg,1,midg; midg,igrid,midg -0.1825186 -0.2334201 1,midg,midg; igrid,midg,midg -0.1589447 -0.4040945 gauss-seidel spectral radius is 0.9993285 estimated iterations to convergence 304 setup time was (sec) 2.690000 now iterating at: 12:15:54 rms-change max change #iterations 11.18612 275.6613 at 10iterations 6.588068 112.3098 at 20iterations 3.892470 67.09610 at 30iterations 2.294678 42.56222 at 40iterations 1.351498 20.77046 at 50iterations 0.7965111 12.53058 at 60iterations 0.4693297 7.416470 at 70iterations 0.2764591 4.625322 at 80iterations 0.1628277 2.839945 at 90iterations 9.5873982E-02 1.728607 at 100iterations 5.6374047E-02 0.9550550 at 110iterations 3.3280000E-02 0.5112405 at 120iterations 1.9609945E-02 0.3015828 at 130iterations 1.1541695E-02 0.1860456 at 140iterations 6.8012066E-03 0.1004956 at 150iterations 4.0026288E-03 6.0270309E-02 at 160iterations 2.3606168E-03 3.9337158E-02 at 170iterations 1.3931089E-03 2.3411751E-02 at 180iterations finished qdiffx linear iterations at : 12:16:11 total time elapsed so far: 19.78000 # loops : 180 mean,max change (kT/e) : 1.3931089E-03 2.3411751E-02 energy calculations done at 19.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.96000 DelPhi exited at 12:16:12 19.963u 0.504s 0:20.78 98.4% 0+0k 0+0io 0pf+0w