Sat Oct 15 13:55:35 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 Sat Oct 15 2011 at 13:55:35 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2668 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: 0.6070942 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): 10.11200 60.97100 ymin,ymax (A): 9.696000 59.24400 zmin,zma (A): 8.711000 67.35100 x,y,z range (A): 50.85900 49.54800 58.64000 scale (grids/A): 0.6070942 object centre (A): 35.54150 34.47000 38.03100 number of atom coordinates read : 2668 total number of charged atoms : 2499 net assigned charge : 2.500011 assigned positive charge : 393.7928 centred at (gu) : 90.60683 88.93122 88.94345 assigned negative charge : -391.2934 centred at (gu) : 90.51176 88.99512 89.02259 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6588 nv = 96 ne = 84 npr = 53847 no. pairs analyzed = 53847 no. exposed pairs = 3563 no. arc points = 24776 no. surface atoms = 1204 nbur = 1464 mkacc time = 9.0000004E-02 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 = 1.456000 m= 300 mr = 3385 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3478 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2516 ## 280 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8090 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1236074E-09 -1.8773259E-09 midg,1,midg; midg,igrid,midg 5.2662563E-09 -1.3178694E-09 1,midg,midg; igrid,midg,midg -2.7308376E-09 6.3466050E-09 gauss-seidel spectral radius is 0.9859663 estimated iterations to convergence 69 setup time was (sec) 0.4100000 now iterating at: 13:55:36 rms-change max change #iterations 0.1186772 16.79593 at 10iterations 1.0124327E-02 1.568314 at 20iterations 9.0343755E-04 0.1391678 at 30iterations 9.2944836E-05 1.4446735E-02 at 40iterations 1.3719877E-05 2.8381348E-03 at 50iterations finished qdiffx linear iterations at : 13:55:39 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 1.3719877E-05 2.8381348E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 13:55:39 3.640u 0.214s 0:04.36 88.3% 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 Sat Oct 15 2011 at 13:55:40 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2668 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: 1.821282 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): 10.11200 60.97100 ymin,ymax (A): 9.696000 59.24400 zmin,zma (A): 8.711000 67.35100 x,y,z range (A): 50.85900 49.54800 58.64000 scale (grids/A): 1.821282 object centre (A): 35.54150 34.47000 38.03100 number of atom coordinates read : 2668 total number of charged atoms : 2499 net assigned charge : 2.500011 assigned positive charge : 393.7928 centred at (gu) : 91.82004 86.79325 86.82980 assigned negative charge : -391.2934 centred at (gu) : 91.53497 86.98508 87.06738 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 70981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24776 grid for indexing accessible points = 1.400000 m= 24307 mr = 47481 m= 3491 mr = 17250 m= 175 mr = 2007 m= 4 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 209 time to turn everything in is 0.3800000 number of dielectric boundary points 32157 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 19567 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) : 0.6070942 object centre at (A) : 35.54150 34.47000 38.03100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9852197E-02 -2.0238362E-02 midg,1,midg; midg,igrid,midg 1.5352350E-02 3.9593680E-03 1,midg,midg; igrid,midg,midg -1.0196989E-02 3.4613779E-03 gauss-seidel spectral radius is 0.9985238 estimated iterations to convergence 206 setup time was (sec) 0.6400000 now iterating at: 13:55:40 rms-change max change #iterations 3.923290 172.7562 at 10iterations 1.783286 66.08342 at 20iterations 0.8098866 29.15150 at 30iterations 0.3672472 12.18894 at 40iterations 0.1668722 5.584518 at 50iterations 7.5766563E-02 2.592918 at 60iterations 3.4432840E-02 1.145824 at 70iterations 1.5610013E-02 0.5219762 at 80iterations 7.1019740E-03 0.2245498 at 90iterations 3.2198646E-03 0.1044219 at 100iterations 1.4684105E-03 4.6516418E-02 at 110iterations 6.6811626E-04 2.3745537E-02 at 120iterations finished qdiffx linear iterations at : 13:55:49 total time elapsed so far: 9.060000 # loops : 120 mean,max change (kT/e) : 6.6811626E-04 2.3745537E-02 energy calculations done at 9.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.190000 DelPhi exited at 13:55:49 9.190u 0.287s 0:09.76 97.0% 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 Sat Oct 15 2011 at 13:55:49 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2668 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: 2.731924 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): 10.11200 60.97100 ymin,ymax (A): 9.696000 59.24400 zmin,zma (A): 8.711000 67.35100 x,y,z range (A): 50.85900 49.54800 58.64000 scale (grids/A): 2.731924 object centre (A): 35.54150 34.47000 38.03100 number of atom coordinates read : 2668 total number of charged atoms : 2499 net assigned charge : 2.500011 assigned positive charge : 393.7928 centred at (gu) : 92.72986 85.18974 85.24465 assigned negative charge : -391.2934 centred at (gu) : 92.30247 85.47755 85.60104 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 164340 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24776 grid for indexing accessible points = 1.400000 m= 79346 mr = 115891 m= 27320 mr = 63158 m= 6010 mr = 21370 m= 737 mr = 4308 m= 44 mr = 430 m= 0 mr = 12 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 675 time to turn everything in is 0.9500000 number of dielectric boundary points 72628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 19989 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) : 1.821282 object centre at (A) : 35.54150 34.47000 38.03100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6726637 -0.2527041 midg,1,midg; midg,igrid,midg 0.1128391 6.4748950E-02 1,midg,midg; igrid,midg,midg -0.1283198 5.1171817E-02 gauss-seidel spectral radius is 0.9992363 estimated iterations to convergence 286 setup time was (sec) 1.240000 now iterating at: 13:55:51 rms-change max change #iterations 9.341226 292.4875 at 10iterations 5.390546 115.8315 at 20iterations 3.090898 67.11093 at 30iterations 1.766125 43.82393 at 40iterations 1.010160 20.14414 at 50iterations 0.5757402 11.45711 at 60iterations 0.3282453 6.446627 at 70iterations 0.1868498 3.766397 at 80iterations 0.1064627 1.938889 at 90iterations 6.0543973E-02 1.235353 at 100iterations 3.4458384E-02 0.7029114 at 110iterations 1.9615512E-02 0.3571253 at 120iterations 1.1148958E-02 0.2037439 at 130iterations 6.3381670E-03 0.1211548 at 140iterations 3.5950034E-03 6.9021702E-02 at 150iterations 2.0451108E-03 4.1502953E-02 at 160iterations 1.1650865E-03 2.2834778E-02 at 170iterations 6.6200132E-04 1.2783051E-02 at 180iterations finished qdiffx linear iterations at : 13:56:04 total time elapsed so far: 14.72000 # loops : 180 mean,max change (kT/e) : 6.6200132E-04 1.2783051E-02 energy calculations done at 14.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.85000 DelPhi exited at 13:56:05 14.847u 0.308s 0:15.46 97.9% 0+0k 0+0io 0pf+0w