Tue Oct 11 06:06:49 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 Tue Oct 11 2011 at 06:06:49 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2045 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7362065 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): -18.09900 30.25700 ymin,ymax (A): -11.70500 30.56600 zmin,zma (A): -8.532000 38.14700 x,y,z range (A): 48.35600 42.27100 46.67900 scale (grids/A): 0.7362065 object centre (A): 6.079000 9.430500 14.80750 number of atom coordinates read : 2045 total number of charged atoms : 1915 net assigned charge : 6.025010 assigned positive charge : 311.9290 centred at (gu) : 89.94160 89.85453 91.20061 assigned negative charge : -305.9041 centred at (gu) : 89.86081 89.77222 91.08324 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7644 nv = 96 ne = 84 npr = 40703 no. pairs analyzed = 40703 no. exposed pairs = 2530 no. arc points = 17408 no. surface atoms = 856 nbur = 1189 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 525 mr = 4410 m= 1 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2600000 number of dielectric boundary points 3662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1587 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8115 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8324804E-09 2.5169038E-07 midg,1,midg; midg,igrid,midg 2.2528553E-08 1.6532886E-07 1,midg,midg; igrid,midg,midg 2.3658345E-08 1.6669780E-07 gauss-seidel spectral radius is 0.9903739 estimated iterations to convergence 83 setup time was (sec) 0.5400000 now iterating at: 06:06:50 rms-change max change #iterations 0.2398345 33.06120 at 10iterations 3.2632165E-02 4.412570 at 20iterations 4.6161776E-03 0.5545998 at 30iterations 7.8258419E-04 9.8136902E-02 at 40iterations 1.8930031E-04 2.4295807E-02 at 50iterations finished qdiffx linear iterations at : 06:06:54 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 1.8930031E-04 2.4295807E-02 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 06:06:55 4.377u 0.405s 0:05.06 94.2% 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 06:06:55 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2045 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.208619 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): -18.09900 30.25700 ymin,ymax (A): -11.70500 30.56600 zmin,zma (A): -8.532000 38.14700 x,y,z range (A): 48.35600 42.27100 46.67900 scale (grids/A): 2.208619 object centre (A): 6.079000 9.430500 14.80750 number of atom coordinates read : 2045 total number of charged atoms : 1915 net assigned charge : 6.025010 assigned positive charge : 311.9290 centred at (gu) : 89.82458 89.56355 93.60182 assigned negative charge : -305.9041 centred at (gu) : 89.58254 89.31679 93.24975 start vw surface at 0.1000000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 80814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17408 grid for indexing accessible points = 1.400000 m= 33903 mr = 57725 m= 7213 mr = 26152 m= 733 mr = 4957 m= 39 mr = 388 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 207 time to turn everything in is 0.6700000 number of dielectric boundary points 33475 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15234 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) : 0.7362065 object centre at (A) : 6.079000 9.430500 14.80750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4056553E-02 5.2477755E-02 midg,1,midg; midg,igrid,midg 2.8963938E-02 2.6563261E-02 1,midg,midg; igrid,midg,midg 4.3134023E-02 3.3133741E-02 gauss-seidel spectral radius is 0.9989060 estimated iterations to convergence 239 setup time was (sec) 0.9800000 now iterating at: 06:06:56 rms-change max change #iterations 4.922470 190.9236 at 10iterations 2.493845 83.32590 at 20iterations 1.270623 38.54535 at 30iterations 0.6458200 18.87021 at 40iterations 0.3263000 8.984571 at 50iterations 0.1665501 5.588120 at 60iterations 8.4285244E-02 2.421841 at 70iterations 4.3062389E-02 1.104980 at 80iterations 2.2053391E-02 0.7750473 at 90iterations 1.1275646E-02 0.3198547 at 100iterations 5.8251307E-03 0.1797416 at 110iterations 3.0480917E-03 8.7815285E-02 at 120iterations finished qdiffx linear iterations at : 06:07:05 total time elapsed so far: 10.54000 # loops : 120 mean,max change (kT/e) : 3.0480917E-03 8.7815285E-02 energy calculations done at 10.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.71000 DelPhi exited at 06:07:06 10.711u 0.447s 0:11.58 96.2% 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 06:07:06 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2045 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.312929 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): -18.09900 30.25700 ymin,ymax (A): -11.70500 30.56600 zmin,zma (A): -8.532000 38.14700 x,y,z range (A): 48.35600 42.27100 46.67900 scale (grids/A): 3.312929 object centre (A): 6.079000 9.430500 14.80750 number of atom coordinates read : 2045 total number of charged atoms : 1915 net assigned charge : 6.025010 assigned positive charge : 311.9290 centred at (gu) : 89.73704 89.34537 95.40270 assigned negative charge : -305.9041 centred at (gu) : 89.37387 88.97520 94.87468 start vw surface at 0.1000000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 186139 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17408 grid for indexing accessible points = 1.400000 m= 103968 mr = 138743 m= 44856 mr = 87286 m= 13625 mr = 37312 m= 2963 mr = 10704 m= 400 mr = 2166 m= 26 mr = 244 m= 0 mr = 10 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 686 time to turn everything in is 2.120000 number of dielectric boundary points 75512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 15320 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) : 2.208619 object centre at (A) : 6.079000 9.430500 14.80750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4824017 0.4724095 midg,1,midg; midg,igrid,midg 0.2501636 0.1349483 1,midg,midg; igrid,midg,midg 0.2588572 0.1359010 gauss-seidel spectral radius is 0.9993165 estimated iterations to convergence 302 setup time was (sec) 2.460000 now iterating at: 06:07:09 rms-change max change #iterations 10.78305 305.1129 at 10iterations 6.422481 132.5417 at 20iterations 3.821037 70.84656 at 30iterations 2.272530 44.35139 at 40iterations 1.348400 22.88769 at 50iterations 0.7972061 12.72507 at 60iterations 0.4726727 8.955128 at 70iterations 0.2783748 4.886848 at 80iterations 0.1646367 2.804591 at 90iterations 9.7379170E-02 1.585930 at 100iterations 5.7646431E-02 0.9523087 at 110iterations 3.4273863E-02 0.6219101 at 120iterations 2.0544916E-02 0.3771172 at 130iterations 1.2461074E-02 0.2303429 at 140iterations 7.7750660E-03 0.1407013 at 150iterations 5.0450382E-03 0.1072206 at 160iterations 3.4533476E-03 6.2355042E-02 at 170iterations 2.5136576E-03 4.7115326E-02 at 180iterations finished qdiffx linear iterations at : 06:07:25 total time elapsed so far: 18.31000 # loops : 180 mean,max change (kT/e) : 2.5136576E-03 4.7115326E-02 energy calculations done at 18.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.48000 DelPhi exited at 06:07:25 18.480u 0.481s 0:19.23 98.5% 0+0k 0+0io 0pf+0w