Tue Oct 11 03:19:33 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 03:19:33 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2982 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5950391 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): -37.77700 20.78300 ymin,ymax (A): -38.74500 19.77900 zmin,zma (A): -67.42300 -7.595000 x,y,z range (A): 58.56000 58.52400 59.82800 scale (grids/A): 0.5950391 object centre (A): -8.497001 -9.483001 -37.50900 number of atom coordinates read : 2982 total number of charged atoms : 2829 net assigned charge : -2.499985 assigned positive charge : 441.9292 centred at (gu) : 89.77704 87.99660 90.57223 assigned negative charge : -444.4302 centred at (gu) : 89.83053 88.03266 90.53292 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7310 nv = 96 ne = 84 npr = 57462 no. pairs analyzed = 57462 no. exposed pairs = 4243 no. arc points = 29866 no. surface atoms = 1409 nbur = 1573 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 347 mr = 3621 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 4024 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3069 ## 342 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9003 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0666808E-09 5.1709048E-10 midg,1,midg; midg,igrid,midg 5.6682092E-10 -1.4243097E-09 1,midg,midg; igrid,midg,midg 9.9902131E-10 -2.7224056E-09 gauss-seidel spectral radius is 0.9854339 estimated iterations to convergence 68 setup time was (sec) 0.5400000 now iterating at: 03:19:34 rms-change max change #iterations 0.1079908 20.87838 at 10iterations 9.0658274E-03 1.587292 at 20iterations 7.5097592E-04 0.1194572 at 30iterations 6.7749148E-05 9.1662407E-03 at 40iterations 7.5082257E-06 1.0719299E-03 at 50iterations finished qdiffx linear iterations at : 03:19:36 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 7.5082257E-06 1.0719299E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 03:19:37 3.163u 0.151s 0:03.72 88.9% 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 03:19:37 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2982 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.785117 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): -37.77700 20.78300 ymin,ymax (A): -38.74500 19.77900 zmin,zma (A): -67.42300 -7.595000 x,y,z range (A): 58.56000 58.52400 59.82800 scale (grids/A): 1.785117 object centre (A): -8.497001 -9.483001 -37.50900 number of atom coordinates read : 2982 total number of charged atoms : 2829 net assigned charge : -2.499985 assigned positive charge : 441.9292 centred at (gu) : 89.33054 83.98901 91.71592 assigned negative charge : -444.4302 centred at (gu) : 89.49126 84.09768 91.59830 start vw surface at 0.2200000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 79380 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29866 grid for indexing accessible points = 1.400000 m= 26336 mr = 52380 m= 3366 mr = 17949 m= 146 mr = 1712 m= 2 mr = 31 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 0.6100000 number of dielectric boundary points 37158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 241 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 22048 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) : 0.5950391 object centre at (A) : -8.497001 -9.483001 -37.50900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0027544E-02 -2.1090202E-02 midg,1,midg; midg,igrid,midg -7.6572369E-03 -3.9525788E-02 1,midg,midg; igrid,midg,midg 2.5453942E-02 -5.0278474E-03 gauss-seidel spectral radius is 0.9985108 estimated iterations to convergence 206 setup time was (sec) 0.9000000 now iterating at: 03:19:38 rms-change max change #iterations 4.044009 161.0430 at 10iterations 1.815921 69.54456 at 20iterations 0.8182126 29.30011 at 30iterations 0.3699881 12.24183 at 40iterations 0.1671264 5.822091 at 50iterations 7.5493820E-02 2.427534 at 60iterations 3.4076888E-02 1.211472 at 70iterations 1.5389576E-02 0.4992828 at 80iterations 6.9697201E-03 0.2259951 at 90iterations 3.1711124E-03 0.1117344 at 100iterations 1.4300960E-03 4.5841217E-02 at 110iterations 6.4774073E-04 2.0935893E-02 at 120iterations finished qdiffx linear iterations at : 03:19:44 total time elapsed so far: 6.870000 # loops : 120 mean,max change (kT/e) : 6.4774073E-04 2.0935893E-02 energy calculations done at 6.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.050000 DelPhi exited at 03:19:45 7.050u 0.185s 0:07.52 96.1% 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 03:19:45 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2982 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.677676 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): -37.77700 20.78300 ymin,ymax (A): -38.74500 19.77900 zmin,zma (A): -67.42300 -7.595000 x,y,z range (A): 58.56000 58.52400 59.82800 scale (grids/A): 2.677676 object centre (A): -8.497001 -9.483001 -37.50900 number of atom coordinates read : 2982 total number of charged atoms : 2829 net assigned charge : -2.499985 assigned positive charge : 441.9292 centred at (gu) : 88.99554 80.98342 92.57363 assigned negative charge : -444.4302 centred at (gu) : 89.23676 81.14642 92.39749 start vw surface at 0.2200000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 183800 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29866 grid for indexing accessible points = 1.400000 m= 87379 mr = 128154 m= 28161 mr = 68438 m= 5506 mr = 21139 m= 569 mr = 3638 m= 31 mr = 289 m= 0 mr = 5 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.420000 number of dielectric boundary points 83783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.540000 number of grid points assigned charge 22629 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) : 1.785117 object centre at (A) : -8.497001 -9.483001 -37.50900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5313003 -0.2184683 midg,1,midg; midg,igrid,midg -3.2389395E-02 -0.7274891 1,midg,midg; igrid,midg,midg 0.2474955 -6.4098470E-02 gauss-seidel spectral radius is 0.9992524 estimated iterations to convergence 289 setup time was (sec) 1.690000 now iterating at: 03:19:47 rms-change max change #iterations 10.13364 357.3952 at 10iterations 6.042489 156.0941 at 20iterations 3.557241 83.22404 at 30iterations 2.074226 54.76048 at 40iterations 1.206648 23.31269 at 50iterations 0.6989450 15.43898 at 60iterations 0.4036348 7.331957 at 70iterations 0.2327121 4.504543 at 80iterations 0.1341315 2.495783 at 90iterations 7.7155389E-02 1.379550 at 100iterations 4.4285990E-02 0.8628235 at 110iterations 2.5424711E-02 0.4585381 at 120iterations 1.4567069E-02 0.2536449 at 130iterations 8.3711836E-03 0.1474304 at 140iterations 4.7912616E-03 9.5706940E-02 at 150iterations 2.7461371E-03 5.2085161E-02 at 160iterations 1.5793465E-03 3.1368256E-02 at 170iterations 9.0480177E-04 1.6519547E-02 at 180iterations finished qdiffx linear iterations at : 03:19:56 total time elapsed so far: 11.21000 # loops : 180 mean,max change (kT/e) : 9.0480177E-04 1.6519547E-02 energy calculations done at 11.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.38000 DelPhi exited at 03:19:57 11.381u 0.192s 0:11.95 96.8% 0+0k 0+0io 0pf+0w