Sat Oct 8 14:08:40 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 Sat Oct 8 2011 at 14:08:40 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2962 !!! WARNING: NAP 316 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6285310 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): -11.28800 43.48200 ymin,ymax (A): 10.36400 55.62400 zmin,zma (A): 35.96400 92.60400 x,y,z range (A): 54.77000 45.26000 56.64000 scale (grids/A): 0.6285310 object centre (A): 16.09700 32.99400 64.28400 number of atom coordinates read : 2962 total number of charged atoms : 2816 net assigned charge : -0.9999920 assigned positive charge : 443.4556 centred at (gu) : 89.15046 89.48643 92.17216 assigned negative charge : -444.4565 centred at (gu) : 89.15382 89.39135 92.10303 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7963 nv = 96 ne = 84 npr = 60987 no. pairs analyzed = 60987 no. exposed pairs = 3459 no. arc points = 23801 no. surface atoms = 1176 nbur = 1786 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 4700 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3631 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2328 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9537 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9072484E-09 8.9814431E-09 midg,1,midg; midg,igrid,midg -1.1679285E-08 7.0894006E-09 1,midg,midg; igrid,midg,midg -9.7479524E-10 -1.2236085E-09 gauss-seidel spectral radius is 0.9869183 estimated iterations to convergence 72 setup time was (sec) 0.6700000 now iterating at: 14:08:41 rms-change max change #iterations 0.1468909 22.52333 at 10iterations 1.4432292E-02 1.896099 at 20iterations 1.4905948E-03 0.1955967 at 30iterations 1.8983433E-04 2.5695801E-02 at 40iterations 3.5833942E-05 5.4655075E-03 at 50iterations finished qdiffx linear iterations at : 14:08:45 total time elapsed so far: 5.050000 # loops : 50 mean,max change (kT/e) : 3.5833942E-05 5.4655075E-03 energy calculations done at 5.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.230000 DelPhi exited at 14:08:46 5.236u 0.471s 0:05.97 95.4% 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 8 2011 at 14:08:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2962 !!! WARNING: NAP 316 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.885593 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): -11.28800 43.48200 ymin,ymax (A): 10.36400 55.62400 zmin,zma (A): 35.96400 92.60400 x,y,z range (A): 54.77000 45.26000 56.64000 scale (grids/A): 1.885593 object centre (A): 16.09700 32.99400 64.28400 number of atom coordinates read : 2962 total number of charged atoms : 2816 net assigned charge : -0.9999920 assigned positive charge : 443.4556 centred at (gu) : 87.45054 88.45850 96.51581 assigned negative charge : -444.4565 centred at (gu) : 87.46133 88.17405 96.30911 start vw surface at 0.1300000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87349 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23801 grid for indexing accessible points = 1.400000 m= 32859 mr = 63614 m= 4798 mr = 24977 m= 241 mr = 2921 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 144 time to turn everything in is 0.7200000 number of dielectric boundary points 33663 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 161 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 22117 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) : 0.6285310 object centre at (A) : 16.09700 32.99400 64.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2887665E-02 8.9345807E-03 midg,1,midg; midg,igrid,midg -5.0707217E-03 1.3489254E-02 1,midg,midg; igrid,midg,midg -1.1724240E-02 7.4351421E-03 gauss-seidel spectral radius is 0.9986405 estimated iterations to convergence 215 setup time was (sec) 1.080000 now iterating at: 14:08:47 rms-change max change #iterations 4.536948 202.9269 at 10iterations 2.130103 71.04094 at 20iterations 1.002069 29.96811 at 30iterations 0.4688263 14.32384 at 40iterations 0.2210139 6.381977 at 50iterations 0.1035735 3.319023 at 60iterations 4.8670050E-02 1.523592 at 70iterations 2.2878632E-02 0.6498413 at 80iterations 1.0802701E-02 0.3300581 at 90iterations 5.0708838E-03 0.1528187 at 100iterations 2.3905227E-03 7.1327209E-02 at 110iterations 1.1273071E-03 3.3845901E-02 at 120iterations finished qdiffx linear iterations at : 14:08:59 total time elapsed so far: 13.22000 # loops : 120 mean,max change (kT/e) : 1.1273071E-03 3.3845901E-02 energy calculations done at 13.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 14:09:00 13.391u 0.535s 0:14.20 98.0% 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 8 2011 at 14:09:00 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2962 !!! WARNING: NAP 316 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.828390 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): -11.28800 43.48200 ymin,ymax (A): 10.36400 55.62400 zmin,zma (A): 35.96400 92.60400 x,y,z range (A): 54.77000 45.26000 56.64000 scale (grids/A): 2.828390 object centre (A): 16.09700 32.99400 64.28400 number of atom coordinates read : 2962 total number of charged atoms : 2816 net assigned charge : -0.9999920 assigned positive charge : 443.4556 centred at (gu) : 86.17570 87.68774 99.77354 assigned negative charge : -444.4565 centred at (gu) : 86.19189 87.26093 99.46374 start vw surface at 0.1300000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 202013 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23801 grid for indexing accessible points = 1.400000 m= 107100 mr = 153136 m= 38255 mr = 89767 m= 8416 mr = 31156 m= 1001 mr = 6214 m= 37 mr = 621 m= 0 mr = 4 time to grow re-entrant surface = 1.180000 no. cavity mid-points inaccessible to solvent = 476 time to turn everything in is 1.900000 number of dielectric boundary points 75924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 22525 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) : 1.885593 object centre at (A) : 16.09700 32.99400 64.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4917321E-02 0.1322925 midg,1,midg; midg,igrid,midg -2.3815924E-02 0.1655456 1,midg,midg; igrid,midg,midg 9.1959881E-03 0.2677774 gauss-seidel spectral radius is 0.9992642 estimated iterations to convergence 291 setup time was (sec) 2.270000 now iterating at: 14:09:03 rms-change max change #iterations 10.60413 377.9291 at 10iterations 6.221924 135.5885 at 20iterations 3.618737 73.71347 at 30iterations 2.105673 40.01543 at 40iterations 1.220870 22.14870 at 50iterations 0.7056317 13.29341 at 60iterations 0.4091634 6.941998 at 70iterations 0.2361476 4.264500 at 80iterations 0.1365160 2.366287 at 90iterations 7.8856386E-02 1.421261 at 100iterations 4.5516800E-02 0.7401295 at 110iterations 2.6203034E-02 0.4521847 at 120iterations 1.5104556E-02 0.2548218 at 130iterations 8.7213116E-03 0.1458054 at 140iterations 5.0501889E-03 9.0946198E-02 at 150iterations 2.9154904E-03 5.0935745E-02 at 160iterations 1.6914689E-03 2.9039383E-02 at 170iterations 9.8697958E-04 1.7303467E-02 at 180iterations finished qdiffx linear iterations at : 14:09:22 total time elapsed so far: 21.38000 # loops : 180 mean,max change (kT/e) : 9.8697958E-04 1.7303467E-02 energy calculations done at 21.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.54000 DelPhi exited at 14:09:22 21.546u 0.583s 0:22.40 98.7% 0+0k 0+0io 0pf+0w