Sun Oct 9 21:02:07 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 Sun Oct 9 2011 at 21:02:07 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 = 2575 !!! WARNING: SEP 142 has a net charge of -0.4750 !!! WARNING: CYS 261 has a net charge of 0.5000 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: 0.6626831 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): -8.413000 38.49900 ymin,ymax (A): -27.42300 26.29800 zmin,zma (A): -12.73300 40.44700 x,y,z range (A): 46.91199 53.72100 53.18000 scale (grids/A): 0.6626831 object centre (A): 15.04300 -0.5625000 13.85700 number of atom coordinates read : 2575 total number of charged atoms : 2429 net assigned charge : 5.025008 assigned positive charge : 389.6179 centred at (gu) : 89.78543 90.15272 90.29218 assigned negative charge : -384.5936 centred at (gu) : 89.70034 90.11686 90.32079 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7509 nv = 96 ne = 84 npr = 52000 no. pairs analyzed = 52000 no. exposed pairs = 3183 no. arc points = 22680 no. surface atoms = 1088 nbur = 1487 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4018 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3000000 number of dielectric boundary points 3867 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2252 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8935 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8647249E-08 8.2133154E-09 midg,1,midg; midg,igrid,midg 6.0600418E-09 2.1974335E-08 1,midg,midg; igrid,midg,midg -4.4749053E-09 3.0145834E-08 gauss-seidel spectral radius is 0.9881973 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 21:02:07 rms-change max change #iterations 0.1712077 27.22855 at 10iterations 1.8398371E-02 2.816273 at 20iterations 1.9656429E-03 0.2544098 at 30iterations 2.1191131E-04 3.1289101E-02 at 40iterations 2.2606331E-05 2.9850006E-03 at 50iterations finished qdiffx linear iterations at : 21:02:10 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 2.2606331E-05 2.9850006E-03 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 21:02:11 3.330u 0.144s 0:03.81 91.0% 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 Sun Oct 9 2011 at 21:02:11 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 = 2575 !!! WARNING: SEP 142 has a net charge of -0.4750 !!! WARNING: CYS 261 has a net charge of 0.5000 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: 1.988049 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): -8.413000 38.49900 ymin,ymax (A): -27.42300 26.29800 zmin,zma (A): -12.73300 40.44700 x,y,z range (A): 46.91199 53.72100 53.18000 scale (grids/A): 1.988049 object centre (A): 15.04300 -0.5625000 13.85700 number of atom coordinates read : 2575 total number of charged atoms : 2429 net assigned charge : 5.025008 assigned positive charge : 389.6179 centred at (gu) : 89.35564 90.45729 90.87591 assigned negative charge : -384.5936 centred at (gu) : 89.10078 90.35023 90.96229 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 80664 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22680 grid for indexing accessible points = 1.400000 m= 29027 mr = 55059 m= 4759 mr = 21136 m= 356 mr = 2873 m= 2 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1018 time to turn everything in is 0.6100000 number of dielectric boundary points 35592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 19209 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) : 0.6626831 object centre at (A) : 15.04300 -0.5625000 13.85700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1420082E-02 -1.6940560E-02 midg,1,midg; midg,igrid,midg 3.5596967E-02 3.5421882E-02 1,midg,midg; igrid,midg,midg -1.0042868E-02 1.6671915E-02 gauss-seidel spectral radius is 0.9987348 estimated iterations to convergence 223 setup time was (sec) 0.8800000 now iterating at: 21:02:12 rms-change max change #iterations 4.579982 188.9457 at 10iterations 2.200120 74.08878 at 20iterations 1.056509 30.04762 at 30iterations 0.5078993 15.39158 at 40iterations 0.2446897 6.977869 at 50iterations 0.1175588 3.468822 at 60iterations 5.6524247E-02 1.645306 at 70iterations 2.7210658E-02 0.7951989 at 80iterations 1.3103562E-02 0.4436874 at 90iterations 6.3213413E-03 0.2010803 at 100iterations 3.0385717E-03 9.5733643E-02 at 110iterations 1.4644288E-03 4.4250488E-02 at 120iterations finished qdiffx linear iterations at : 21:02:18 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 1.4644288E-03 4.4250488E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.520000 DelPhi exited at 21:02:19 7.524u 0.178s 0:07.97 96.4% 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 Sun Oct 9 2011 at 21:02:19 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 = 2575 !!! WARNING: SEP 142 has a net charge of -0.4750 !!! WARNING: CYS 261 has a net charge of 0.5000 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: 2.982074 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): -8.413000 38.49900 ymin,ymax (A): -27.42300 26.29800 zmin,zma (A): -12.73300 40.44700 x,y,z range (A): 46.91199 53.72100 53.18000 scale (grids/A): 2.982074 object centre (A): 15.04300 -0.5625000 13.85700 number of atom coordinates read : 2575 total number of charged atoms : 2429 net assigned charge : 5.025008 assigned positive charge : 389.6179 centred at (gu) : 89.03327 90.68593 91.31402 assigned negative charge : -384.5936 centred at (gu) : 88.65116 90.52551 91.44346 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 186325 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22680 grid for indexing accessible points = 1.400000 m= 92985 mr = 133227 m= 34382 mr = 75672 m= 8678 mr = 27423 m= 1457 mr = 6328 m= 102 mr = 960 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 3269 time to turn everything in is 1.510000 number of dielectric boundary points 80280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 19431 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) : 1.988049 object centre at (A) : 15.04300 -0.5625000 13.85700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2868404 -0.3474262 midg,1,midg; midg,igrid,midg 0.4690133 0.4420598 1,midg,midg; igrid,midg,midg -8.7150574E-02 0.1425140 gauss-seidel spectral radius is 0.9992880 estimated iterations to convergence 296 setup time was (sec) 1.810000 now iterating at: 21:02:21 rms-change max change #iterations 10.52722 330.3807 at 10iterations 6.179636 132.0805 at 20iterations 3.608063 75.55303 at 30iterations 2.105873 40.83704 at 40iterations 1.227310 20.90020 at 50iterations 0.7130523 13.18380 at 60iterations 0.4148869 7.161584 at 70iterations 0.2414484 3.964336 at 80iterations 0.1396829 2.605350 at 90iterations 8.1142157E-02 1.565521 at 100iterations 4.7243875E-02 0.7830353 at 110iterations 2.7389342E-02 0.4786367 at 120iterations 1.5881695E-02 0.2608471 at 130iterations 9.2148483E-03 0.1537046 at 140iterations 5.3482638E-03 9.9305153E-02 at 150iterations 3.1032478E-03 5.2268028E-02 at 160iterations 1.8016809E-03 3.0475616E-02 at 170iterations 1.0452747E-03 1.7813683E-02 at 180iterations finished qdiffx linear iterations at : 21:02:31 total time elapsed so far: 12.07000 # loops : 180 mean,max change (kT/e) : 1.0452747E-03 1.7813683E-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) 12.26000 DelPhi exited at 21:02:31 12.259u 0.181s 0:12.79 97.1% 0+0k 0+0io 0pf+0w