Tue Oct 11 08:37:11 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 08:37:12 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 = 2127 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: 0.7051879 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): -36.87300 10.25600 ymin,ymax (A): 12.20400 49.36400 zmin,zma (A): -26.68200 23.80100 x,y,z range (A): 47.12900 37.16000 50.48300 scale (grids/A): 0.7051879 object centre (A): -13.30850 30.78400 -1.440500 number of atom coordinates read : 2127 total number of charged atoms : 1999 net assigned charge : 6.500009 assigned positive charge : 325.1109 centred at (gu) : 89.36311 89.48485 90.86629 assigned negative charge : -318.6111 centred at (gu) : 89.22765 89.50549 90.92950 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7065 nv = 96 ne = 84 npr = 42617 no. pairs analyzed = 42617 no. exposed pairs = 2616 no. arc points = 17472 no. surface atoms = 894 nbur = 1233 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4056 m= 7 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3398 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1641 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 8000 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0135009E-08 2.5773652E-08 midg,1,midg; midg,igrid,midg 6.9039466E-08 3.8880938E-08 1,midg,midg; igrid,midg,midg -1.5402092E-08 1.0318512E-07 gauss-seidel spectral radius is 0.9895195 estimated iterations to convergence 80 setup time was (sec) 0.4500000 now iterating at: 08:37:12 rms-change max change #iterations 0.2032560 26.87000 at 10iterations 2.4801577E-02 3.759272 at 20iterations 3.2879664E-03 0.4491653 at 30iterations 5.3017063E-04 6.7546606E-02 at 40iterations 1.2413866E-04 1.7042160E-02 at 50iterations finished qdiffx linear iterations at : 08:37:14 total time elapsed so far: 2.850000 # loops : 50 mean,max change (kT/e) : 1.2413866E-04 1.7042160E-02 energy calculations done at 2.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.020000 DelPhi exited at 08:37:15 3.024u 0.146s 0:03.48 90.8% 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 08:37:15 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 = 2127 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: 2.115564 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): -36.87300 10.25600 ymin,ymax (A): 12.20400 49.36400 zmin,zma (A): -26.68200 23.80100 x,y,z range (A): 47.12900 37.16000 50.48300 scale (grids/A): 2.115564 object centre (A): -13.30850 30.78400 -1.440500 number of atom coordinates read : 2127 total number of charged atoms : 1999 net assigned charge : 6.500009 assigned positive charge : 325.1109 centred at (gu) : 88.08908 88.45467 92.59874 assigned negative charge : -318.6111 centred at (gu) : 87.68313 88.51645 92.78858 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74943 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17472 grid for indexing accessible points = 1.400000 m= 29996 mr = 53360 m= 5763 mr = 22699 m= 545 mr = 3863 m= 14 mr = 283 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 31056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 77 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 15861 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) : 0.7051879 object centre at (A) : -13.30850 30.78400 -1.440500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6197586E-02 2.6607145E-02 midg,1,midg; midg,igrid,midg 2.9680625E-02 9.2453109E-03 1,midg,midg; igrid,midg,midg 1.2532066E-02 2.8083872E-02 gauss-seidel spectral radius is 0.9988257 estimated iterations to convergence 231 setup time was (sec) 0.8000000 now iterating at: 08:37:16 rms-change max change #iterations 4.650383 189.2393 at 10iterations 2.304144 76.63837 at 20iterations 1.139444 38.27985 at 30iterations 0.5670528 17.57099 at 40iterations 0.2819746 8.700413 at 50iterations 0.1396241 4.318829 at 60iterations 6.9289535E-02 2.073830 at 70iterations 3.4454625E-02 1.057570 at 80iterations 1.7144004E-02 0.5331650 at 90iterations 8.5453689E-03 0.2520142 at 100iterations 4.2793234E-03 0.1285253 at 110iterations 2.1573820E-03 7.3011160E-02 at 120iterations finished qdiffx linear iterations at : 08:37:22 total time elapsed so far: 6.970000 # loops : 120 mean,max change (kT/e) : 2.1573820E-03 7.3011160E-02 energy calculations done at 6.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.150000 DelPhi exited at 08:37:23 7.151u 0.152s 0:07.75 94.1% 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 08:37:23 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 = 2127 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: 3.173346 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): -36.87300 10.25600 ymin,ymax (A): 12.20400 49.36400 zmin,zma (A): -26.68200 23.80100 x,y,z range (A): 47.12900 37.16000 50.48300 scale (grids/A): 3.173346 object centre (A): -13.30850 30.78400 -1.440500 number of atom coordinates read : 2127 total number of charged atoms : 1999 net assigned charge : 6.500009 assigned positive charge : 325.1109 centred at (gu) : 87.13376 87.68204 93.89805 assigned negative charge : -318.6111 centred at (gu) : 86.52463 87.77481 94.18272 start vw surface at 0.1400000 fill in re-entrant regions at 0.7700000 boundary points on vw surface= 173021 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17472 grid for indexing accessible points = 1.400000 m= 93467 mr = 128643 m= 38003 mr = 77875 m= 11114 mr = 31208 m= 2203 mr = 8611 m= 268 mr = 1618 m= 11 mr = 155 m= 0 mr = 3 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.710000 number of dielectric boundary points 69974 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 15992 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) : 2.115564 object centre at (A) : -13.30850 30.78400 -1.440500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3136754 0.1696604 midg,1,midg; midg,igrid,midg 0.2512836 4.9279720E-02 1,midg,midg; igrid,midg,midg 0.2596388 0.2445319 gauss-seidel spectral radius is 0.9992943 estimated iterations to convergence 297 setup time was (sec) 1.990000 now iterating at: 08:37:25 rms-change max change #iterations 10.42755 321.1788 at 10iterations 6.187202 159.7914 at 20iterations 3.655748 80.16154 at 30iterations 2.156891 44.16759 at 40iterations 1.268050 26.61215 at 50iterations 0.7462404 14.11250 at 60iterations 0.4375820 8.685039 at 70iterations 0.2562869 4.805483 at 80iterations 0.1502769 2.716937 at 90iterations 8.8174865E-02 1.761602 at 100iterations 5.1749237E-02 1.100826 at 110iterations 3.0363576E-02 0.5590820 at 120iterations 1.7948868E-02 0.3216839 at 130iterations 1.0697124E-02 0.1966286 at 140iterations 6.5080044E-03 0.1332321 at 150iterations 4.0722000E-03 6.8912506E-02 at 160iterations 2.6681868E-03 5.0333142E-02 at 170iterations 1.8487109E-03 3.1579018E-02 at 180iterations finished qdiffx linear iterations at : 08:37:34 total time elapsed so far: 11.33000 # loops : 180 mean,max change (kT/e) : 1.8487109E-03 3.1579018E-02 energy calculations done at 11.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.50000 DelPhi exited at 08:37:35 11.504u 0.173s 0:12.12 96.2% 0+0k 0+0io 0pf+0w