Sun Oct 9 13:28:13 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+sph2.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 = amb2.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 13:28:13 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2356 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6861593 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): -6.921000 44.15700 ymin,ymax (A): -14.08700 37.79600 zmin,zma (A): 1.801000 44.89000 x,y,z range (A): 51.07800 51.88300 43.08900 scale (grids/A): 0.6861593 object centre (A): 18.61800 11.85450 23.34550 number of atom coordinates read : 2356 total number of charged atoms : 2216 net assigned charge : 4.500012 assigned positive charge : 361.1492 centred at (gu) : 89.71621 90.89196 90.87112 assigned negative charge : -356.6496 centred at (gu) : 89.68620 91.02422 90.96472 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7579 nv = 96 ne = 84 npr = 46771 no. pairs analyzed = 46771 no. exposed pairs = 2902 no. arc points = 20551 no. surface atoms = 976 nbur = 1380 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 460 mr = 4256 m= 1 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1926 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8547 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.6660762E-08 -1.1348659E-08 midg,1,midg; midg,igrid,midg 5.7360754E-08 -2.7859715E-08 1,midg,midg; igrid,midg,midg 1.3733154E-08 3.1951089E-08 gauss-seidel spectral radius is 0.9889652 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 13:28:14 rms-change max change #iterations 0.1895613 25.30632 at 10iterations 2.2930345E-02 3.270142 at 20iterations 3.2204005E-03 0.4826965 at 30iterations 7.1285682E-04 0.1181335 at 40iterations 2.1779418E-04 3.6495209E-02 at 50iterations finished qdiffx linear iterations at : 13:28:17 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 2.1779418E-04 3.6495209E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 13:28:17 3.318u 0.156s 0:03.75 92.2% 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 13:28:17 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2356 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.058478 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): -6.921000 44.15700 ymin,ymax (A): -14.08700 37.79600 zmin,zma (A): 1.801000 44.89000 x,y,z range (A): 51.07800 51.88300 43.08900 scale (grids/A): 2.058478 object centre (A): 18.61800 11.85450 23.34550 number of atom coordinates read : 2356 total number of charged atoms : 2216 net assigned charge : 4.500012 assigned positive charge : 361.1492 centred at (gu) : 89.14825 92.67533 92.61253 assigned negative charge : -356.6496 centred at (gu) : 89.05841 93.07261 92.89399 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 80806 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20551 grid for indexing accessible points = 1.400000 m= 31241 mr = 56656 m= 5568 mr = 23363 m= 509 mr = 3567 m= 12 mr = 251 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 770 time to turn everything in is 0.3900000 number of dielectric boundary points 34299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17551 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) : 0.6861593 object centre at (A) : 18.61800 11.85450 23.34550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1905300E-02 9.8639624E-03 midg,1,midg; midg,igrid,midg 1.2928120E-02 -4.7300436E-02 1,midg,midg; igrid,midg,midg 4.1205250E-02 -1.0758098E-02 gauss-seidel spectral radius is 0.9988024 estimated iterations to convergence 229 setup time was (sec) 0.6000000 now iterating at: 13:28:18 rms-change max change #iterations 4.773232 233.0885 at 10iterations 2.331465 77.04625 at 20iterations 1.147636 36.32550 at 30iterations 0.5646807 19.70946 at 40iterations 0.2772530 8.570866 at 50iterations 0.1369227 4.290466 at 60iterations 6.7352518E-02 2.034386 at 70iterations 3.3305515E-02 0.9895592 at 80iterations 1.6569709E-02 0.4781570 at 90iterations 8.3194971E-03 0.2514162 at 100iterations 4.2497884E-03 0.1528549 at 110iterations 2.2591709E-03 7.7117920E-02 at 120iterations finished qdiffx linear iterations at : 13:28:25 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 2.2591709E-03 7.7117920E-02 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.700000 DelPhi exited at 13:28:25 7.698u 0.199s 0:08.19 96.2% 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 13:28:25 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2356 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.087717 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): -6.921000 44.15700 ymin,ymax (A): -14.08700 37.79600 zmin,zma (A): 1.801000 44.89000 x,y,z range (A): 51.07800 51.88300 43.08900 scale (grids/A): 3.087717 object centre (A): 18.61800 11.85450 23.34550 number of atom coordinates read : 2356 total number of charged atoms : 2216 net assigned charge : 4.500012 assigned positive charge : 361.1492 centred at (gu) : 88.72234 94.01292 93.91879 assigned negative charge : -356.6496 centred at (gu) : 88.58743 94.60906 94.34106 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 186382 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20551 grid for indexing accessible points = 1.400000 m= 98768 mr = 136604 m= 38134 mr = 81440 m= 10191 mr = 31009 m= 2035 mr = 7754 m= 245 mr = 1493 m= 7 mr = 147 m= 0 mr = 2 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 2701 time to turn everything in is 1.200000 number of dielectric boundary points 77313 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 17726 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) : 2.058478 object centre at (A) : 18.61800 11.85450 23.34550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4861683 -2.6531696E-02 midg,1,midg; midg,igrid,midg 0.2496890 -0.5921797 1,midg,midg; igrid,midg,midg 0.3947759 -0.4283358 gauss-seidel spectral radius is 0.9992920 estimated iterations to convergence 297 setup time was (sec) 1.420000 now iterating at: 13:28:27 rms-change max change #iterations 10.68603 441.8947 at 10iterations 6.320392 153.8370 at 20iterations 3.722653 85.10144 at 30iterations 2.185045 38.39374 at 40iterations 1.283371 23.06505 at 50iterations 0.7541648 14.22152 at 60iterations 0.4408444 7.388683 at 70iterations 0.2576730 4.338997 at 80iterations 0.1511756 2.559074 at 90iterations 8.8230491E-02 1.651215 at 100iterations 5.1663816E-02 0.8910084 at 110iterations 3.0509675E-02 0.6013613 at 120iterations 1.8071327E-02 0.3397217 at 130iterations 1.0901636E-02 0.1930161 at 140iterations 6.7604985E-03 0.1376076 at 150iterations 4.3765306E-03 9.2712402E-02 at 160iterations 2.9996780E-03 6.8191528E-02 at 170iterations 2.1873130E-03 4.9476624E-02 at 180iterations finished qdiffx linear iterations at : 13:28:38 total time elapsed so far: 12.60000 # loops : 180 mean,max change (kT/e) : 2.1873130E-03 4.9476624E-02 energy calculations done at 12.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 13:28:39 12.756u 0.200s 0:13.22 97.9% 0+0k 0+0io 0pf+0w