Tue Oct 11 05:57:59 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 Tue Oct 11 2011 at 05:57:59 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 = 2081 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: 0.7367855 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): -17.86100 30.45700 ymin,ymax (A): -11.64400 30.55600 zmin,zma (A): -8.456000 38.04400 x,y,z range (A): 48.31800 42.20000 46.50000 scale (grids/A): 0.7367855 object centre (A): 6.298000 9.455999 14.79400 number of atom coordinates read : 2081 total number of charged atoms : 1953 net assigned charge : 6.500008 assigned positive charge : 316.5540 centred at (gu) : 90.01120 89.75997 90.97867 assigned negative charge : -310.0542 centred at (gu) : 89.95007 89.67101 90.86240 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7721 nv = 96 ne = 84 npr = 42037 no. pairs analyzed = 42037 no. exposed pairs = 2503 no. arc points = 17035 no. surface atoms = 855 nbur = 1226 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 539 mr = 4560 m= 4 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.2700000 number of dielectric boundary points 3597 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1516 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8271 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.3087182E-10 2.5458002E-07 midg,1,midg; midg,igrid,midg 2.4057465E-08 1.7901242E-07 1,midg,midg; igrid,midg,midg 4.9189392E-08 1.6224357E-07 gauss-seidel spectral radius is 0.9903893 estimated iterations to convergence 83 setup time was (sec) 0.5300000 now iterating at: 05:58:00 rms-change max change #iterations 0.2376956 36.42925 at 10iterations 3.2273538E-02 4.526062 at 20iterations 4.4330019E-03 0.5311928 at 30iterations 6.6258141E-04 8.4152222E-02 at 40iterations 1.2386157E-04 1.4259338E-02 at 50iterations finished qdiffx linear iterations at : 05:58:03 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 1.2386157E-04 1.4259338E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 05:58:03 3.630u 0.211s 0:04.26 90.1% 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 05:58:03 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 = 2081 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.210356 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): -17.86100 30.45700 ymin,ymax (A): -11.64400 30.55600 zmin,zma (A): -8.456000 38.04400 x,y,z range (A): 48.31800 42.20000 46.50000 scale (grids/A): 2.210356 object centre (A): 6.298000 9.455999 14.79400 number of atom coordinates read : 2081 total number of charged atoms : 1953 net assigned charge : 6.500008 assigned positive charge : 316.5540 centred at (gu) : 90.03341 89.28012 92.93598 assigned negative charge : -310.0542 centred at (gu) : 89.85039 89.01297 92.58734 start vw surface at 0.2100000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 81367 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17035 grid for indexing accessible points = 1.400000 m= 34237 mr = 58475 m= 7242 mr = 26502 m= 750 mr = 4985 m= 32 mr = 424 m= 0 mr = 3 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1255 time to turn everything in is 0.7100000 number of dielectric boundary points 33239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 15542 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) : 0.7367855 object centre at (A) : 6.298000 9.455999 14.79400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8139576E-02 4.6834037E-02 midg,1,midg; midg,igrid,midg 2.9816125E-02 3.0998105E-02 1,midg,midg; igrid,midg,midg 4.9719047E-02 3.5972357E-02 gauss-seidel spectral radius is 0.9989082 estimated iterations to convergence 239 setup time was (sec) 1.040000 now iterating at: 05:58:05 rms-change max change #iterations 4.924195 186.1145 at 10iterations 2.489315 83.17304 at 20iterations 1.271046 37.03051 at 30iterations 0.6454780 19.43064 at 40iterations 0.3261098 9.814299 at 50iterations 0.1666492 4.809152 at 60iterations 8.4572099E-02 2.307701 at 70iterations 4.2987503E-02 1.315052 at 80iterations 2.1937676E-02 0.6980209 at 90iterations 1.1204045E-02 0.3553658 at 100iterations 5.7445476E-03 0.1761360 at 110iterations 2.9423272E-03 8.0636978E-02 at 120iterations finished qdiffx linear iterations at : 05:58:12 total time elapsed so far: 8.350000 # loops : 120 mean,max change (kT/e) : 2.9423272E-03 8.0636978E-02 energy calculations done at 8.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.550000 DelPhi exited at 05:58:13 8.553u 0.235s 0:09.09 96.5% 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 05:58:13 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 = 2081 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 3.315535 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): -17.86100 30.45700 ymin,ymax (A): -11.64400 30.55600 zmin,zma (A): -8.456000 38.04400 x,y,z range (A): 48.31800 42.20000 46.50000 scale (grids/A): 3.315535 object centre (A): 6.298000 9.455999 14.79400 number of atom coordinates read : 2081 total number of charged atoms : 1953 net assigned charge : 6.500008 assigned positive charge : 316.5540 centred at (gu) : 90.05013 88.92033 94.40395 assigned negative charge : -310.0542 centred at (gu) : 89.77556 88.51954 93.88107 start vw surface at 0.2100000 fill in re-entrant regions at 0.9800000 boundary points on vw surface= 186983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17035 grid for indexing accessible points = 1.400000 m= 104821 mr = 139894 m= 45076 mr = 88267 m= 14076 mr = 37681 m= 3073 mr = 11182 m= 431 mr = 2327 m= 18 mr = 258 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 4183 time to turn everything in is 2.160000 number of dielectric boundary points 74869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.320000 number of grid points assigned charge 15624 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) : 2.210356 object centre at (A) : 6.298000 9.455999 14.79400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5378739 0.4006116 midg,1,midg; midg,igrid,midg 0.2552161 0.1613559 1,midg,midg; igrid,midg,midg 0.3003694 0.1636791 gauss-seidel spectral radius is 0.9993154 estimated iterations to convergence 302 setup time was (sec) 2.520000 now iterating at: 05:58:15 rms-change max change #iterations 10.76803 326.7526 at 10iterations 6.402054 124.9099 at 20iterations 3.800056 85.59346 at 30iterations 2.258029 41.83603 at 40iterations 1.338128 25.35069 at 50iterations 0.7904635 12.85348 at 60iterations 0.4672334 7.895367 at 70iterations 0.2757016 4.493187 at 80iterations 0.1625853 2.623200 at 90iterations 9.6096978E-02 1.560026 at 100iterations 5.6737710E-02 1.042722 at 110iterations 3.3642851E-02 0.5439358 at 120iterations 2.0013511E-02 0.3357468 at 130iterations 1.2045447E-02 0.2032433 at 140iterations 7.3792748E-03 0.1287870 at 150iterations 4.6536676E-03 8.1298828E-02 at 160iterations 3.0603998E-03 5.3565979E-02 at 170iterations 2.1300633E-03 3.7521362E-02 at 180iterations finished qdiffx linear iterations at : 05:58:27 total time elapsed so far: 14.23000 # loops : 180 mean,max change (kT/e) : 2.1300633E-03 3.7521362E-02 energy calculations done at 14.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.43000 DelPhi exited at 05:58:28 14.433u 0.250s 0:15.09 97.2% 0+0k 0+0io 0pf+0w