Tue Oct 11 03:34:49 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 Tue Oct 11 2011 at 03:34:50 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2262 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: GLU 460 has a net charge of -2.0000 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: 0.5598453 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): -27.62500 35.96400 ymin,ymax (A): -7.047000 41.24600 zmin,zma (A): 4.420000 51.41200 x,y,z range (A): 63.58900 48.29300 46.99200 scale (grids/A): 0.5598453 object centre (A): 4.169500 17.09950 27.91600 number of atom coordinates read : 2262 total number of charged atoms : 2176 net assigned charge : -6.485980 assigned positive charge : 338.8441 centred at (gu) : 92.10738 90.12832 89.98047 assigned negative charge : -345.3307 centred at (gu) : 92.14159 90.20376 89.87222 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4716 nv = 96 ne = 84 npr = 45490 no. pairs analyzed = 45490 no. exposed pairs = 2902 no. arc points = 21059 no. surface atoms = 985 nbur = 1277 mkacc time = 0.1300000 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 = 1.512000 m= 205 mr = 2361 m= 0 mr = 7 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2553 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2116 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6076 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6151507E-09 2.3460703E-10 midg,1,midg; midg,igrid,midg -3.7022548E-11 -1.3632514E-09 1,midg,midg; igrid,midg,midg -2.3975155E-10 -1.6053123E-09 gauss-seidel spectral radius is 0.9834884 estimated iterations to convergence 64 setup time was (sec) 0.5800000 now iterating at: 03:34:50 rms-change max change #iterations 7.2494224E-02 14.50271 at 10iterations 5.1687481E-03 0.9840012 at 20iterations 3.6344104E-04 6.1123848E-02 at 30iterations 2.5853920E-05 4.8236847E-03 at 40iterations 1.8212068E-06 3.6621094E-04 at 50iterations finished qdiffx linear iterations at : 03:34:54 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 1.8212068E-06 3.6621094E-04 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 03:34:54 4.051u 0.247s 0:04.60 93.2% 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 Tue Oct 11 2011 at 03:34:54 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2262 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: GLU 460 has a net charge of -2.0000 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: 1.679536 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): -27.62500 35.96400 ymin,ymax (A): -7.047000 41.24600 zmin,zma (A): 4.420000 51.41200 x,y,z range (A): 63.58900 48.29300 46.99200 scale (grids/A): 1.679536 object centre (A): 4.169500 17.09950 27.91600 number of atom coordinates read : 2262 total number of charged atoms : 2176 net assigned charge : -6.485980 assigned positive charge : 338.8441 centred at (gu) : 96.32153 90.38422 89.94080 assigned negative charge : -345.3307 centred at (gu) : 96.42466 90.61098 89.61662 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 51427 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21059 grid for indexing accessible points = 1.400000 m= 15256 mr = 33915 m= 1563 mr = 10291 m= 43 mr = 785 m= 0 mr = 1 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 103 time to turn everything in is 0.4600000 number of dielectric boundary points 23297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 202 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 16815 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) : 0.5598453 object centre at (A) : 4.169500 17.09950 27.91600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2976624E-03 5.9483210E-03 midg,1,midg; midg,igrid,midg 1.7777936E-03 -1.1087434E-02 1,midg,midg; igrid,midg,midg -2.2967642E-03 -2.3313396E-02 gauss-seidel spectral radius is 0.9982094 estimated iterations to convergence 188 setup time was (sec) 0.7600000 now iterating at: 03:34:55 rms-change max change #iterations 3.069814 137.6921 at 10iterations 1.277797 53.72185 at 20iterations 0.5390949 22.53484 at 30iterations 0.2254101 9.429638 at 40iterations 9.4626360E-02 3.613735 at 50iterations 3.9447196E-02 1.682180 at 60iterations 1.6564107E-02 0.6529636 at 70iterations 6.9203395E-03 0.2612267 at 80iterations 2.9086615E-03 0.1272163 at 90iterations 1.2205930E-03 4.7142029E-02 at 100iterations 5.1034027E-04 2.1812916E-02 at 110iterations 2.1380089E-04 8.4991455E-03 at 120iterations finished qdiffx linear iterations at : 03:35:03 total time elapsed so far: 8.840000 # loops : 120 mean,max change (kT/e) : 2.1380089E-04 8.4991455E-03 energy calculations done at 8.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.020000 DelPhi exited at 03:35:04 9.021u 0.285s 0:09.60 96.8% 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 Tue Oct 11 2011 at 03:35:04 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2262 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: GLU 460 has a net charge of -2.0000 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: 2.519304 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): -27.62500 35.96400 ymin,ymax (A): -7.047000 41.24600 zmin,zma (A): 4.420000 51.41200 x,y,z range (A): 63.58900 48.29300 46.99200 scale (grids/A): 2.519304 object centre (A): 4.169500 17.09950 27.91600 number of atom coordinates read : 2262 total number of charged atoms : 2176 net assigned charge : -6.485980 assigned positive charge : 338.8441 centred at (gu) : 99.48229 90.57632 89.91126 assigned negative charge : -345.3307 centred at (gu) : 99.63683 90.91646 89.42490 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 119630 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21059 grid for indexing accessible points = 1.400000 m= 52557 mr = 83347 m= 15014 mr = 40981 m= 2452 mr = 11273 m= 169 mr = 1620 m= 2 mr = 67 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.6200000 no. cavity mid-points inaccessible to solvent = 371 time to turn everything in is 1.110000 number of dielectric boundary points 52536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 17390 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) : 1.679536 object centre at (A) : 4.169500 17.09950 27.91600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.5835283E-02 0.1279021 midg,1,midg; midg,igrid,midg 3.3007894E-02 -0.1485690 1,midg,midg; igrid,midg,midg -0.1008433 -0.2514893 gauss-seidel spectral radius is 0.9991250 estimated iterations to convergence 267 setup time was (sec) 1.420000 now iterating at: 03:35:06 rms-change max change #iterations 7.793317 284.3494 at 10iterations 4.313794 127.1608 at 20iterations 2.375479 57.64121 at 30iterations 1.305119 32.47498 at 40iterations 0.7163256 16.82506 at 50iterations 0.3928586 10.00233 at 60iterations 0.2139018 5.279245 at 70iterations 0.1174672 2.524448 at 80iterations 6.3973784E-02 1.415633 at 90iterations 3.4878775E-02 0.9221001 at 100iterations 1.9020645E-02 0.4226542 at 110iterations 1.0419125E-02 0.2316971 at 120iterations 5.6790463E-03 0.1370263 at 130iterations 3.0999414E-03 7.2194099E-02 at 140iterations 1.6924395E-03 4.0077209E-02 at 150iterations 9.2276314E-04 2.0843506E-02 at 160iterations 5.0425145E-04 1.1081696E-02 at 170iterations 2.7484307E-04 6.1993152E-03 at 180iterations finished qdiffx linear iterations at : 03:35:19 total time elapsed so far: 14.39000 # loops : 180 mean,max change (kT/e) : 2.7484307E-04 6.1993152E-03 energy calculations done at 14.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.56000 DelPhi exited at 03:35:19 14.561u 0.307s 0:15.23 97.5% 0+0k 0+0io 0pf+0w