Wed Feb 15 08:55:09 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:09 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 = 1384 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.8499057 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): -9.937000 24.54200 ymin,ymax (A): -9.076000 30.65200 zmin,zma (A): -6.478000 35.40900 x,y,z range (A): 34.47900 39.72800 41.88700 scale (grids/A): 0.8499057 object centre (A): 7.302500 10.78800 14.46550 number of atom coordinates read : 1384 total number of charged atoms : 1253 net assigned charge : -0.4999973 assigned positive charge : 203.9293 centred at (gu) : 90.44019 88.66191 90.84328 assigned negative charge : -204.4291 centred at (gu) : 90.47967 88.76783 90.51894 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6737 nv = 96 ne = 84 npr = 30794 no. pairs analyzed = 30794 no. exposed pairs = 1706 no. arc points = 12457 no. surface atoms = 575 nbur = 809 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 604 mr = 3764 m= 9 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2100000 number of dielectric boundary points 3448 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 808 ## 68 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6337 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3969245E-06 1.5640293E-06 midg,1,midg; midg,igrid,midg 4.9409130E-07 -4.6044426E-07 1,midg,midg; igrid,midg,midg 8.4870280E-08 -2.8945465E-07 gauss-seidel spectral radius is 0.9926933 estimated iterations to convergence 95 setup time was (sec) 0.4400000 now iterating at: 08:55:10 rms-change max change #iterations 0.3289588 46.79771 at 10iterations 5.6491043E-02 6.737212 at 20iterations 9.8339813E-03 1.327515 at 30iterations 1.6721726E-03 0.2250495 at 40iterations 2.9020983E-04 3.7448883E-02 at 50iterations finished qdiffx linear iterations at : 08:55:13 total time elapsed so far: 3.090000 # loops : 50 mean,max change (kT/e) : 2.9020983E-04 3.7448883E-02 energy calculations done at 3.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 08:55:13 3.273u 0.165s 0:03.89 88.1% 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 Wed Feb 15 2012 at 08:55:13 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 = 1384 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.549717 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): -9.937000 24.54200 ymin,ymax (A): -9.076000 30.65200 zmin,zma (A): -6.478000 35.40900 x,y,z range (A): 34.47900 39.72800 41.88700 scale (grids/A): 2.549717 object centre (A): 7.302500 10.78800 14.46550 number of atom coordinates read : 1384 total number of charged atoms : 1253 net assigned charge : -0.4999973 assigned positive charge : 203.9293 centred at (gu) : 91.32064 85.98603 92.53006 assigned negative charge : -204.4291 centred at (gu) : 91.43898 86.30354 91.55677 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 69185 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12457 grid for indexing accessible points = 1.400000 m= 29457 mr = 47258 m= 7675 mr = 22841 m= 1243 mr = 5397 m= 142 mr = 731 m= 7 mr = 86 m= 0 mr = 4 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 399 time to turn everything in is 0.6000000 number of dielectric boundary points 31392 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 10015 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) : 0.8499057 object centre at (A) : 7.302500 10.78800 14.46550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7355885E-02 9.1894135E-02 midg,1,midg; midg,igrid,midg 1.7398205E-02 -6.9785558E-02 1,midg,midg; igrid,midg,midg -1.3720174E-02 8.9178495E-03 gauss-seidel spectral radius is 0.9990709 estimated iterations to convergence 259 setup time was (sec) 0.8900000 now iterating at: 08:55:14 rms-change max change #iterations 4.985733 278.3639 at 10iterations 2.665686 106.3216 at 20iterations 1.421964 39.54283 at 30iterations 0.7598920 26.61724 at 40iterations 0.4071411 14.83999 at 50iterations 0.2179385 6.343224 at 60iterations 0.1163860 3.224684 at 70iterations 6.2362097E-02 1.920318 at 80iterations 3.3095751E-02 0.9395103 at 90iterations 1.7766777E-02 0.5502930 at 100iterations 9.4973026E-03 0.2839575 at 110iterations 5.0643208E-03 0.1444550 at 120iterations finished qdiffx linear iterations at : 08:55:21 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 5.0643208E-03 0.1444550 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 08:55:22 7.662u 0.163s 0:08.36 93.5% 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 Wed Feb 15 2012 at 08:55:22 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 = 1384 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.824576 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): -9.937000 24.54200 ymin,ymax (A): -9.076000 30.65200 zmin,zma (A): -6.478000 35.40900 x,y,z range (A): 34.47900 39.72800 41.88700 scale (grids/A): 3.824576 object centre (A): 7.302500 10.78800 14.46550 number of atom coordinates read : 1384 total number of charged atoms : 1253 net assigned charge : -0.4999973 assigned positive charge : 203.9293 centred at (gu) : 91.98109 83.97890 93.79517 assigned negative charge : -204.4291 centred at (gu) : 92.15848 84.45534 92.33511 start vw surface at 0.1400000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 158818 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12457 grid for indexing accessible points = 1.400000 m= 86980 mr = 113409 m= 41395 mr = 72721 m= 15486 mr = 34957 m= 4394 mr = 12342 m= 1131 mr = 3232 m= 211 mr = 872 m= 18 mr = 150 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 1333 time to turn everything in is 1.910000 number of dielectric boundary points 70737 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 10020 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) : 2.549717 object centre at (A) : 7.302500 10.78800 14.46550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1076487 0.5244682 midg,1,midg; midg,igrid,midg 0.1382671 -0.5311861 1,midg,midg; igrid,midg,midg -0.1365514 0.1482634 gauss-seidel spectral radius is 0.9993377 estimated iterations to convergence 306 setup time was (sec) 2.230000 now iterating at: 08:55:24 rms-change max change #iterations 10.22428 273.2088 at 10iterations 6.064123 135.4944 at 20iterations 3.581645 65.03611 at 30iterations 2.116009 39.59070 at 40iterations 1.251062 22.92429 at 50iterations 0.7413896 12.13552 at 60iterations 0.4382093 7.152405 at 70iterations 0.2585064 4.902420 at 80iterations 0.1531004 2.564247 at 90iterations 9.0486050E-02 1.526207 at 100iterations 5.3676147E-02 1.070752 at 110iterations 3.1804524E-02 0.5766907 at 120iterations 1.8822584E-02 0.3479538 at 130iterations 1.1182538E-02 0.1951180 at 140iterations 6.6974289E-03 0.1149979 at 150iterations 4.0128357E-03 6.9000244E-02 at 160iterations 2.4398696E-03 4.1861534E-02 at 170iterations 1.5112766E-03 2.8331757E-02 at 180iterations finished qdiffx linear iterations at : 08:55:35 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 1.5112766E-03 2.8331757E-02 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 08:55:37 13.224u 0.229s 0:14.90 90.2% 0+0k 0+0io 0pf+0w