Sat Oct 15 13:17:46 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 Sat Oct 15 2011 at 13:17:46 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5404 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 0.5211764 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): 3.236000 68.98300 ymin,ymax (A): -8.963000 53.32100 zmin,zma (A): -1.371000 66.93600 x,y,z range (A): 65.74700 62.28400 68.30701 scale (grids/A): 0.5211764 object centre (A): 36.10950 22.17900 32.78250 number of atom coordinates read : 5404 total number of charged atoms : 5246 net assigned charge : 5.754036 assigned positive charge : 836.5331 centred at (gu) : 88.10793 89.28934 88.62376 assigned negative charge : -830.7852 centred at (gu) : 88.02029 89.29601 88.55723 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9428 nv = 96 ne = 84 npr = 109726 no. pairs analyzed = 109726 no. exposed pairs = 6273 no. arc points = 43029 no. surface atoms = 2126 nbur = 3278 mkacc time = 0.2900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 332 mr = 5303 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 4439 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4307 ## 587 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 12621 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4875474E-10 3.1554973E-10 midg,1,midg; midg,igrid,midg 2.0756694E-10 9.3129282E-11 1,midg,midg; igrid,midg,midg -4.5303072E-10 3.3577918E-10 gauss-seidel spectral radius is 0.9812078 estimated iterations to convergence 60 setup time was (sec) 0.8800000 now iterating at: 13:17:47 rms-change max change #iterations 8.9580916E-02 13.76185 at 10iterations 9.8308269E-03 1.501015 at 20iterations 3.6274032E-03 0.5904503 at 30iterations 1.5635309E-03 0.2582359 at 40iterations 6.7891239E-04 0.1120605 at 50iterations finished qdiffx linear iterations at : 13:17:52 total time elapsed so far: 5.520000 # loops : 50 mean,max change (kT/e) : 6.7891239E-04 0.1120605 energy calculations done at 5.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.690000 DelPhi exited at 13:17:53 5.693u 0.461s 0:06.56 93.7% 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 Sat Oct 15 2011 at 13:17:53 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5404 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 1.563529 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): 3.236000 68.98300 ymin,ymax (A): -8.963000 53.32100 zmin,zma (A): -1.371000 66.93600 x,y,z range (A): 65.74700 62.28400 68.30701 scale (grids/A): 1.563529 object centre (A): 36.10950 22.17900 32.78250 number of atom coordinates read : 5404 total number of charged atoms : 5246 net assigned charge : 5.754036 assigned positive charge : 836.5331 centred at (gu) : 84.32235 87.86672 85.86995 assigned negative charge : -830.7852 centred at (gu) : 84.06044 87.88776 85.67168 start vw surface at 0.1900000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 106943 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43029 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 33893 mr = 77253 m= 3202 mr = 23795 m= 75 mr = 1520 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9100000 number of dielectric boundary points 41538 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 542 ## 6 charges are in solution ## iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 39673 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) : 0.5211764 object centre at (A) : 36.10950 22.17900 32.78250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6371625E-02 2.4009887E-02 midg,1,midg; midg,igrid,midg 1.8331006E-02 5.7426183E-03 1,midg,midg; igrid,midg,midg -9.5727276E-03 4.2141583E-03 gauss-seidel spectral radius is 0.9982370 estimated iterations to convergence 189 setup time was (sec) 1.270000 now iterating at: 13:17:55 rms-change max change #iterations 4.377569 162.9897 at 10iterations 1.849013 58.48494 at 20iterations 0.7830964 21.92078 at 30iterations 0.3321156 9.274216 at 40iterations 0.1419606 4.186516 at 50iterations 6.1352685E-02 1.931213 at 60iterations 2.7547937E-02 0.8120499 at 70iterations 1.3476509E-02 0.4561462 at 80iterations 7.6695252E-03 0.2764168 at 90iterations 4.9740053E-03 0.1670609 at 100iterations 3.5169229E-03 0.1151009 at 110iterations 2.5740876E-03 8.3843231E-02 at 120iterations finished qdiffx linear iterations at : 13:18:07 total time elapsed so far: 13.44000 # loops : 120 mean,max change (kT/e) : 2.5740876E-03 8.3843231E-02 energy calculations done at 13.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.60000 DelPhi exited at 13:18:07 13.608u 0.547s 0:14.58 96.9% 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 Sat Oct 15 2011 at 13:18:07 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5404 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.345294 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): 3.236000 68.98300 ymin,ymax (A): -8.963000 53.32100 zmin,zma (A): -1.371000 66.93600 x,y,z range (A): 65.74700 62.28400 68.30701 scale (grids/A): 2.345294 object centre (A): 36.10950 22.17900 32.78250 number of atom coordinates read : 5404 total number of charged atoms : 5246 net assigned charge : 5.754036 assigned positive charge : 836.5331 centred at (gu) : 81.48333 86.79956 83.80444 assigned negative charge : -830.7852 centred at (gu) : 81.09056 86.83165 83.50742 start vw surface at 0.2000000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 249258 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43029 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 119356 mr = 188597 m= 32900 mr = 96326 m= 4756 mr = 24731 m= 290 mr = 3046 m= 5 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 1.430000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.280000 number of dielectric boundary points 93733 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 2.460000 number of grid points assigned charge 41869 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) : 1.563529 object centre at (A) : 36.10950 22.17900 32.78250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3638184 0.6745681 midg,1,midg; midg,igrid,midg 0.2908868 4.7442909E-02 1,midg,midg; igrid,midg,midg -0.3391656 7.3750384E-02 gauss-seidel spectral radius is 0.9991998 estimated iterations to convergence 279 setup time was (sec) 2.700000 now iterating at: 13:18:11 rms-change max change #iterations 11.47202 289.2568 at 10iterations 6.628093 151.9370 at 20iterations 3.797478 79.09763 at 30iterations 2.161441 41.42493 at 40iterations 1.229172 23.69838 at 50iterations 0.6982551 12.00374 at 60iterations 0.3949704 7.311966 at 70iterations 0.2235534 3.757755 at 80iterations 0.1262097 2.096142 at 90iterations 7.1679331E-02 1.238174 at 100iterations 4.0820591E-02 0.6986135 at 110iterations 2.3541903E-02 0.4215889 at 120iterations 1.3917626E-02 0.2478943 at 130iterations 8.5587166E-03 0.1687317 at 140iterations 5.5686729E-03 0.1231346 at 150iterations 3.8996367E-03 8.3469391E-02 at 160iterations 2.9231401E-03 6.0272217E-02 at 170iterations 2.2889585E-03 4.6821594E-02 at 180iterations finished qdiffx linear iterations at : 13:18:33 total time elapsed so far: 24.15000 # loops : 180 mean,max change (kT/e) : 2.2889585E-03 4.6821594E-02 energy calculations done at 24.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 24.33000 DelPhi exited at 13:18:34 24.331u 0.545s 0:26.06 95.4% 0+0k 0+0io 0pf+0w