Mon Oct 10 13:55:53 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 13:55:54 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 = 2579 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6381758 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): 16.94400 72.72800 ymin,ymax (A): 14.37300 63.50200 zmin,zma (A): 20.75900 65.25400 x,y,z range (A): 55.78400 49.12901 44.49500 scale (grids/A): 0.6381758 object centre (A): 44.83600 38.93750 43.00650 number of atom coordinates read : 2579 total number of charged atoms : 2439 net assigned charge : -1.999993 assigned positive charge : 394.7199 centred at (gu) : 91.14494 91.09599 91.65664 assigned negative charge : -396.7205 centred at (gu) : 91.15404 90.89931 91.72648 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6911 nv = 96 ne = 84 npr = 52328 no. pairs analyzed = 52328 no. exposed pairs = 3135 no. arc points = 23146 no. surface atoms = 1057 nbur = 1522 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 367 mr = 3680 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 13 time to turn everything in is 0.3100000 number of dielectric boundary points 3568 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2298 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8480 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4458427E-09 -1.5463323E-08 midg,1,midg; midg,igrid,midg -2.0123887E-08 2.4081324E-08 1,midg,midg; igrid,midg,midg -1.4392395E-09 -4.9207216E-09 gauss-seidel spectral radius is 0.9872784 estimated iterations to convergence 72 setup time was (sec) 0.5800000 now iterating at: 13:55:54 rms-change max change #iterations 0.1423246 22.02319 at 10iterations 1.3976344E-02 2.314274 at 20iterations 1.3606042E-03 0.2069511 at 30iterations 1.3542337E-04 2.3086309E-02 at 40iterations 1.3390595E-05 1.9836426E-03 at 50iterations finished qdiffx linear iterations at : 13:55:58 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 1.3390595E-05 1.9836426E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.650000 DelPhi exited at 13:55:59 4.655u 0.381s 0:05.35 94.0% 0+0k 0+0io 6pf+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 13:55:59 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 = 2579 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.914528 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): 16.94400 72.72800 ymin,ymax (A): 14.37300 63.50200 zmin,zma (A): 20.75900 65.25400 x,y,z range (A): 55.78400 49.12901 44.49500 scale (grids/A): 1.914528 object centre (A): 44.83600 38.93750 43.00650 number of atom coordinates read : 2579 total number of charged atoms : 2439 net assigned charge : -1.999993 assigned positive charge : 394.7199 centred at (gu) : 93.43446 93.28753 94.96926 assigned negative charge : -396.7205 centred at (gu) : 93.46183 92.69786 95.17926 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74911 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23146 grid for indexing accessible points = 1.400000 m= 25307 mr = 50973 m= 3951 mr = 18413 m= 257 mr = 2418 m= 4 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 3820 time to turn everything in is 0.5900000 number of dielectric boundary points 32515 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 19195 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) : 0.6381758 object centre at (A) : 44.83600 38.93750 43.00650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6531335E-03 -2.1939415E-02 midg,1,midg; midg,igrid,midg -1.6360564E-02 1.3089594E-02 1,midg,midg; igrid,midg,midg 9.6899653E-03 -3.1862531E-02 gauss-seidel spectral radius is 0.9986476 estimated iterations to convergence 215 setup time was (sec) 0.9100000 now iterating at: 13:56:00 rms-change max change #iterations 4.327017 186.3690 at 10iterations 2.032399 70.27424 at 20iterations 0.9511281 29.69320 at 30iterations 0.4459241 14.69411 at 40iterations 0.2096134 7.167839 at 50iterations 9.8136522E-02 2.882911 at 60iterations 4.6268746E-02 1.460889 at 70iterations 2.1678692E-02 0.7442780 at 80iterations 1.0178629E-02 0.3131924 at 90iterations 4.7884211E-03 0.1497149 at 100iterations 2.2477966E-03 6.7354202E-02 at 110iterations 1.0584289E-03 3.5940170E-02 at 120iterations finished qdiffx linear iterations at : 13:56:10 total time elapsed so far: 10.38000 # loops : 120 mean,max change (kT/e) : 1.0584289E-03 3.5940170E-02 energy calculations done at 10.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.55000 DelPhi exited at 13:56:10 10.554u 0.445s 0:11.52 95.3% 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 13:56:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2579 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.871791 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): 16.94400 72.72800 ymin,ymax (A): 14.37300 63.50200 zmin,zma (A): 20.75900 65.25400 x,y,z range (A): 55.78400 49.12901 44.49500 scale (grids/A): 2.871791 object centre (A): 44.83600 38.93750 43.00650 number of atom coordinates read : 2579 total number of charged atoms : 2439 net assigned charge : -1.999993 assigned positive charge : 394.7199 centred at (gu) : 95.15160 94.93119 97.45399 assigned negative charge : -396.7205 centred at (gu) : 95.19263 94.04671 97.76883 start vw surface at 0.1100000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 173288 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23146 grid for indexing accessible points = 1.400000 m= 83334 mr = 123991 m= 28991 mr = 67513 m= 7133 mr = 23030 m= 1137 mr = 5320 m= 88 mr = 778 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 12839 time to turn everything in is 1.590000 number of dielectric boundary points 73294 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 19509 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) : 1.914528 object centre at (A) : 44.83600 38.93750 43.00650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7684126E-02 -0.4065869 midg,1,midg; midg,igrid,midg -0.1347662 0.1541983 1,midg,midg; igrid,midg,midg 0.2135762 -0.1685787 gauss-seidel spectral radius is 0.9992583 estimated iterations to convergence 290 setup time was (sec) 1.900000 now iterating at: 13:56:15 rms-change max change #iterations 10.02923 415.3672 at 10iterations 5.811659 138.1195 at 20iterations 3.339685 60.93494 at 30iterations 1.916463 36.16543 at 40iterations 1.102213 21.71391 at 50iterations 0.6312794 11.76342 at 60iterations 0.3615598 7.497488 at 70iterations 0.2073679 3.777691 at 80iterations 0.1189434 2.264391 at 90iterations 6.8117045E-02 1.277853 at 100iterations 3.8938142E-02 0.7131424 at 110iterations 2.2324936E-02 0.3785744 at 120iterations 1.2831464E-02 0.2296953 at 130iterations 7.3342831E-03 0.1562977 at 140iterations 4.2146062E-03 8.0188751E-02 at 150iterations 2.4153122E-03 4.4250488E-02 at 160iterations 1.3832169E-03 2.6008606E-02 at 170iterations 7.9429772E-04 1.5130043E-02 at 180iterations finished qdiffx linear iterations at : 13:56:31 total time elapsed so far: 17.92000 # loops : 180 mean,max change (kT/e) : 7.9429772E-04 1.5130043E-02 energy calculations done at 17.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.09000 DelPhi exited at 13:56:32 18.096u 0.500s 0:19.03 97.6% 0+0k 0+0io 0pf+0w