Mon Oct 10 14:14:54 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 Mon Oct 10 2011 at 14:14:54 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1603 !!! WARNING: SEP 63 has a net charge of -0.4750 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: GLM 102 has a net charge of -0.0940 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: 0.7229014 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): -6.311000 37.18600 ymin,ymax (A): 1.020000 50.26600 zmin,zma (A): 6.184000 47.56400 x,y,z range (A): 43.49700 49.24600 41.38000 scale (grids/A): 0.7229014 object centre (A): 15.43750 25.64300 26.87400 number of atom coordinates read : 1603 total number of charged atoms : 1459 net assigned charge : -8.543992 assigned positive charge : 234.7932 centred at (gu) : 90.69360 91.50536 90.97443 assigned negative charge : -243.3371 centred at (gu) : 90.71142 91.70525 90.64668 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5777 nv = 96 ne = 84 npr = 33251 no. pairs analyzed = 33251 no. exposed pairs = 2121 no. arc points = 14829 no. surface atoms = 717 nbur = 886 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 3161 m= 1 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.2300000 number of dielectric boundary points 2906 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1166 ## 74 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6028 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3636146E-07 8.4544830E-08 midg,1,midg; midg,igrid,midg 1.0792354E-09 -2.8328782E-07 1,midg,midg; igrid,midg,midg -8.1755957E-08 -1.2734846E-07 gauss-seidel spectral radius is 0.9899817 estimated iterations to convergence 81 setup time was (sec) 0.4500000 now iterating at: 14:14:55 rms-change max change #iterations 0.1976076 28.01006 at 10iterations 2.5260638E-02 4.022305 at 20iterations 3.2303890E-03 0.5131111 at 30iterations 4.0836533E-04 6.5505981E-02 at 40iterations 5.1809406E-05 7.6956749E-03 at 50iterations finished qdiffx linear iterations at : 14:14:57 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 5.1809406E-05 7.6956749E-03 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 14:14:58 3.215u 0.185s 0:03.75 90.4% 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 Mon Oct 10 2011 at 14:14:58 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1603 !!! WARNING: SEP 63 has a net charge of -0.4750 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: GLM 102 has a net charge of -0.0940 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: 2.168704 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): -6.311000 37.18600 ymin,ymax (A): 1.020000 50.26600 zmin,zma (A): 6.184000 47.56400 x,y,z range (A): 43.49700 49.24600 41.38000 scale (grids/A): 2.168704 object centre (A): 15.43750 25.64300 26.87400 number of atom coordinates read : 1603 total number of charged atoms : 1459 net assigned charge : -8.543992 assigned positive charge : 234.7932 centred at (gu) : 92.08076 94.51618 92.92356 assigned negative charge : -243.3371 centred at (gu) : 92.13424 95.11581 91.94015 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 60276 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14829 grid for indexing accessible points = 1.400000 m= 23954 mr = 40697 m= 4772 mr = 18267 m= 402 mr = 3305 m= 6 mr = 192 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 902 time to turn everything in is 0.4600000 number of dielectric boundary points 26949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 11608 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) : 0.7229014 object centre at (A) : 15.43750 25.64300 26.87400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8624875E-02 2.2009907E-02 midg,1,midg; midg,igrid,midg 6.8610976E-03 -7.4372441E-02 1,midg,midg; igrid,midg,midg -4.0339347E-02 -3.8505346E-02 gauss-seidel spectral radius is 0.9988329 estimated iterations to convergence 232 setup time was (sec) 0.7500000 now iterating at: 14:14:59 rms-change max change #iterations 4.229280 191.6277 at 10iterations 2.089959 76.14195 at 20iterations 1.038031 35.12877 at 30iterations 0.5150030 18.25873 at 40iterations 0.2551897 8.175251 at 50iterations 0.1265358 4.255107 at 60iterations 6.2579207E-02 2.042455 at 70iterations 3.1228103E-02 1.058496 at 80iterations 1.5448899E-02 0.4851227 at 90iterations 7.6617813E-03 0.2358131 at 100iterations 3.7989060E-03 0.1228914 at 110iterations 1.8815447E-03 5.9662819E-02 at 120iterations finished qdiffx linear iterations at : 14:15:05 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 1.8815447E-03 5.9662819E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.420000 DelPhi exited at 14:15:06 7.424u 0.228s 0:08.23 92.8% 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 Mon Oct 10 2011 at 14:15:06 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1603 !!! WARNING: SEP 63 has a net charge of -0.4750 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: GLM 102 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.253056 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): -6.311000 37.18600 ymin,ymax (A): 1.020000 50.26600 zmin,zma (A): 6.184000 47.56400 x,y,z range (A): 43.49700 49.24600 41.38000 scale (grids/A): 3.253056 object centre (A): 15.43750 25.64300 26.87400 number of atom coordinates read : 1603 total number of charged atoms : 1459 net assigned charge : -8.543992 assigned positive charge : 234.7932 centred at (gu) : 93.12130 96.77428 94.38529 assigned negative charge : -243.3371 centred at (gu) : 93.20138 97.67375 92.91027 start vw surface at 0.1400000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 138557 reading accessible surface arcs data from file ARCDAT no. of arc points read = 14829 grid for indexing accessible points = 1.400000 m= 73220 mr = 97775 m= 30949 mr = 60665 m= 9084 mr = 25856 m= 1729 mr = 7285 m= 184 mr = 1262 m= 6 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 2929 time to turn everything in is 1.440000 number of dielectric boundary points 60783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 11672 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) : 2.168704 object centre at (A) : 15.43750 25.64300 26.87400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3971227 0.2735425 midg,1,midg; midg,igrid,midg 7.7268519E-02 -0.6552003 1,midg,midg; igrid,midg,midg -0.2916171 -0.1959869 gauss-seidel spectral radius is 0.9992959 estimated iterations to convergence 297 setup time was (sec) 1.740000 now iterating at: 14:15:08 rms-change max change #iterations 9.275416 325.2151 at 10iterations 5.412387 109.5546 at 20iterations 3.170626 59.21108 at 30iterations 1.845253 41.80624 at 40iterations 1.075776 23.65630 at 50iterations 0.6275945 12.38998 at 60iterations 0.3655218 6.634748 at 70iterations 0.2129869 3.861008 at 80iterations 0.1239201 2.423256 at 90iterations 7.1796052E-02 1.322305 at 100iterations 4.1889023E-02 0.8869324 at 110iterations 2.4420671E-02 0.4458897 at 120iterations 1.4189967E-02 0.2883644 at 130iterations 8.2509778E-03 0.1419449 at 140iterations 4.7958405E-03 9.1184616E-02 at 150iterations 2.7895516E-03 5.3076267E-02 at 160iterations 1.6206718E-03 3.0279160E-02 at 170iterations 9.4367337E-04 1.6662598E-02 at 180iterations finished qdiffx linear iterations at : 14:15:18 total time elapsed so far: 12.07000 # loops : 180 mean,max change (kT/e) : 9.4367337E-04 1.6662598E-02 energy calculations done at 12.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.24000 DelPhi exited at 14:15:19 12.241u 0.211s 0:12.94 96.2% 0+0k 0+0io 0pf+0w