Mon Oct 10 10:23:43 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 10:23:44 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 = 2823 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5809684 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): -17.72900 33.77700 ymin,ymax (A): -59.95200 -0.8070000 zmin,zma (A): -1.710000 59.56700 x,y,z range (A): 51.50600 59.14500 61.27700 scale (grids/A): 0.5809684 object centre (A): 8.023998 -30.37950 28.92850 number of atom coordinates read : 2823 total number of charged atoms : 2671 net assigned charge : 5.000015 assigned positive charge : 411.8419 centred at (gu) : 88.48269 88.37917 88.19296 assigned negative charge : -406.8423 centred at (gu) : 88.58656 88.27883 88.08960 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6595 nv = 96 ne = 84 npr = 54144 no. pairs analyzed = 54144 no. exposed pairs = 4298 no. arc points = 31343 no. surface atoms = 1418 nbur = 1405 mkacc time = 0.1200000 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 = 1.484000 m= 314 mr = 2853 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3085 ## 307 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8125 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5633255E-09 2.1521169E-09 midg,1,midg; midg,igrid,midg -1.3964563E-09 2.2045163E-09 1,midg,midg; igrid,midg,midg 4.6921089E-09 -6.8373929E-10 gauss-seidel spectral radius is 0.9847173 estimated iterations to convergence 66 setup time was (sec) 0.5500000 now iterating at: 10:23:44 rms-change max change #iterations 9.1048822E-02 15.80841 at 10iterations 6.9729565E-03 1.067909 at 20iterations 5.6114176E-04 8.7493896E-02 at 30iterations 4.7349280E-05 7.3919296E-03 at 40iterations 5.1547099E-06 7.1144104E-04 at 50iterations finished qdiffx linear iterations at : 10:23:47 total time elapsed so far: 3.160000 # loops : 50 mean,max change (kT/e) : 5.1547099E-06 7.1144104E-04 energy calculations done at 3.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 10:23:48 3.378u 0.220s 0:04.00 89.7% 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 10:23:48 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 = 2823 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: 1.742905 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): -17.72900 33.77700 ymin,ymax (A): -59.95200 -0.8070000 zmin,zma (A): -1.710000 59.56700 x,y,z range (A): 51.50600 59.14500 61.27700 scale (grids/A): 1.742905 object centre (A): 8.023998 -30.37950 28.92850 number of atom coordinates read : 2823 total number of charged atoms : 2671 net assigned charge : 5.000015 assigned positive charge : 411.8419 centred at (gu) : 85.44757 85.13712 84.57865 assigned negative charge : -406.8423 centred at (gu) : 85.75974 84.83625 84.26846 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 70535 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31343 grid for indexing accessible points = 1.400000 m= 21859 mr = 43011 m= 2695 mr = 13794 m= 119 mr = 1057 m= 2 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 252 time to turn everything in is 0.4800000 number of dielectric boundary points 37339 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 247 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 20732 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) : 0.5809684 object centre at (A) : 8.023998 -30.37950 28.92850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3505491E-03 5.3522112E-03 midg,1,midg; midg,igrid,midg 1.8231429E-02 2.9565377E-02 1,midg,midg; igrid,midg,midg 1.1677314E-02 2.1718948E-03 gauss-seidel spectral radius is 0.9984262 estimated iterations to convergence 200 setup time was (sec) 0.7500000 now iterating at: 10:23:49 rms-change max change #iterations 3.649056 158.6962 at 10iterations 1.606417 70.78957 at 20iterations 0.7045880 25.95893 at 30iterations 0.3119812 11.04143 at 40iterations 0.1369644 5.272104 at 50iterations 6.0600840E-02 2.110509 at 60iterations 2.6788197E-02 0.9231453 at 70iterations 1.1842271E-02 0.4368973 at 80iterations 5.2161282E-03 0.2060928 at 90iterations 2.3039966E-03 7.6759338E-02 at 100iterations 1.0190668E-03 3.7879944E-02 at 110iterations 4.5162602E-04 1.4946938E-02 at 120iterations finished qdiffx linear iterations at : 10:23:55 total time elapsed so far: 7.020000 # loops : 120 mean,max change (kT/e) : 4.5162602E-04 1.4946938E-02 energy calculations done at 7.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.180000 DelPhi exited at 10:23:56 7.187u 0.237s 0:08.02 92.3% 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 10:23:56 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 = 2823 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.614358 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): -17.72900 33.77700 ymin,ymax (A): -59.95200 -0.8070000 zmin,zma (A): -1.710000 59.56700 x,y,z range (A): 51.50600 59.14500 61.27700 scale (grids/A): 2.614358 object centre (A): 8.023998 -30.37950 28.92850 number of atom coordinates read : 2823 total number of charged atoms : 2671 net assigned charge : 5.000015 assigned positive charge : 411.8419 centred at (gu) : 83.17125 82.70554 81.86776 assigned negative charge : -406.8423 centred at (gu) : 83.63947 82.25435 81.40264 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 162754 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31343 grid for indexing accessible points = 1.400000 m= 72692 mr = 106066 m= 22694 mr = 53985 m= 3994 mr = 15766 m= 301 mr = 2242 m= 13 mr = 85 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 798 time to turn everything in is 1.210000 number of dielectric boundary points 84304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 21360 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) : 1.742905 object centre at (A) : 8.023998 -30.37950 28.92850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4469888E-02 1.4503522E-02 midg,1,midg; midg,igrid,midg 0.3612806 0.4088078 1,midg,midg; igrid,midg,midg 6.8739884E-02 4.4771127E-02 gauss-seidel spectral radius is 0.9992295 estimated iterations to convergence 284 setup time was (sec) 1.520000 now iterating at: 10:23:57 rms-change max change #iterations 9.304681 290.4525 at 10iterations 5.520851 133.6632 at 20iterations 3.218123 81.28871 at 30iterations 1.872586 43.99659 at 40iterations 1.082569 25.76998 at 50iterations 0.6207339 13.53143 at 60iterations 0.3564036 8.361887 at 70iterations 0.2042450 4.404248 at 80iterations 0.1164250 2.327619 at 90iterations 6.6557705E-02 1.487934 at 100iterations 3.7945259E-02 0.8445777 at 110iterations 2.1597462E-02 0.4425201 at 120iterations 1.2286698E-02 0.2657380 at 130iterations 6.9872043E-03 0.1357789 at 140iterations 3.9699720E-03 7.6433539E-02 at 150iterations 2.2561674E-03 4.6178818E-02 at 160iterations 1.2816569E-03 2.5473595E-02 at 170iterations 7.2876812E-04 1.5621185E-02 at 180iterations finished qdiffx linear iterations at : 10:24:09 total time elapsed so far: 13.21000 # loops : 180 mean,max change (kT/e) : 7.2876812E-04 1.5621185E-02 energy calculations done at 13.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.37000 DelPhi exited at 10:24:10 13.370u 0.251s 0:14.03 97.0% 0+0k 0+0io 0pf+0w