Sat Oct 15 15:34:24 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+sph.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 = amb.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 15:34:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 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: 0.6901365 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): -40.84700 0.2750000 ymin,ymax (A): -27.20700 18.68200 zmin,zma (A): -17.27000 34.31400 x,y,z range (A): 41.12200 45.88900 51.58400 scale (grids/A): 0.6901365 object centre (A): -20.28600 -4.262501 8.521999 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 90.85533 89.86024 89.83464 assigned negative charge : -311.0742 centred at (gu) : 90.88965 89.98021 89.78213 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6732 nv = 96 ne = 84 npr = 42044 no. pairs analyzed = 42044 no. exposed pairs = 2560 no. arc points = 17370 no. surface atoms = 862 nbur = 1227 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 3852 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1679 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7635 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9216165E-08 5.1789794E-08 midg,1,midg; midg,igrid,midg 7.7610039E-08 -3.9545949E-09 1,midg,midg; igrid,midg,midg 4.0242245E-08 2.9049101E-08 gauss-seidel spectral radius is 0.9890603 estimated iterations to convergence 78 setup time was (sec) 0.3600000 now iterating at: 15:34:25 rms-change max change #iterations 0.1748294 25.10212 at 10iterations 2.0838877E-02 2.904915 at 20iterations 2.5808744E-03 0.4066353 at 30iterations 3.9276449E-04 4.8006058E-02 at 40iterations 8.4872649E-05 1.1383057E-02 at 50iterations finished qdiffx linear iterations at : 15:34:31 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 8.4872649E-05 1.1383057E-02 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.770000 DelPhi exited at 15:34:31 3.777u 0.210s 0:07.29 54.5% 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 15:34:31 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.070410 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): -40.84700 0.2750000 ymin,ymax (A): -27.20700 18.68200 zmin,zma (A): -17.27000 34.31400 x,y,z range (A): 41.12200 45.88900 51.58400 scale (grids/A): 2.070410 object centre (A): -20.28600 -4.262501 8.521999 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 92.56608 89.58047 89.50391 assigned negative charge : -311.0742 centred at (gu) : 92.66904 89.94067 89.34635 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71492 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17370 grid for indexing accessible points = 1.400000 m= 27775 mr = 50695 m= 5168 mr = 20956 m= 404 mr = 3374 m= 2 mr = 202 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 29614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 105 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15540 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) : 0.6901365 object centre at (A) : -20.28600 -4.262501 8.521999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7629768E-02 3.8855314E-02 midg,1,midg; midg,igrid,midg 3.6329601E-02 7.5265355E-03 1,midg,midg; igrid,midg,midg 1.4123797E-02 2.2240242E-02 gauss-seidel spectral radius is 0.9987800 estimated iterations to convergence 227 setup time was (sec) 0.6400000 now iterating at: 15:34:32 rms-change max change #iterations 4.366830 180.9985 at 10iterations 2.132073 75.10276 at 20iterations 1.041013 33.13723 at 30iterations 0.5111911 17.56551 at 40iterations 0.2483316 9.261543 at 50iterations 0.1221921 3.879144 at 60iterations 5.9702095E-02 1.889427 at 70iterations 2.9249849E-02 0.9225464 at 80iterations 1.4353422E-02 0.4190941 at 90iterations 7.0571299E-03 0.2350521 at 100iterations 3.4836335E-03 0.1085358 at 110iterations 1.7437065E-03 6.6647768E-02 at 120iterations finished qdiffx linear iterations at : 15:34:48 total time elapsed so far: 8.820000 # loops : 120 mean,max change (kT/e) : 1.7437065E-03 6.6647768E-02 energy calculations done at 8.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.950000 DelPhi exited at 15:34:49 8.956u 0.290s 0:17.38 53.1% 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 Sat Oct 15 2011 at 15:34:49 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.105614 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): -40.84700 0.2750000 ymin,ymax (A): -27.20700 18.68200 zmin,zma (A): -17.27000 34.31400 x,y,z range (A): 41.12200 45.88900 51.58400 scale (grids/A): 3.105614 object centre (A): -20.28600 -4.262501 8.521999 number of atom coordinates read : 2089 total number of charged atoms : 1961 net assigned charge : 6.500009 assigned positive charge : 317.5739 centred at (gu) : 93.84913 89.37061 89.25567 assigned negative charge : -311.0742 centred at (gu) : 94.00374 89.91108 89.01950 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 164922 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17370 grid for indexing accessible points = 1.400000 m= 87449 mr = 121896 m= 34390 mr = 72652 m= 9684 mr = 28238 m= 1810 mr = 7406 m= 157 mr = 1349 m= 1 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.150000 number of dielectric boundary points 66801 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 15684 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) : 2.070410 object centre at (A) : -20.28600 -4.262501 8.521999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3047868 0.2764070 midg,1,midg; midg,igrid,midg 0.3171754 7.6570079E-02 1,midg,midg; igrid,midg,midg 9.1425613E-02 0.2140156 gauss-seidel spectral radius is 0.9992814 estimated iterations to convergence 294 setup time was (sec) 1.410000 now iterating at: 15:34:51 rms-change max change #iterations 9.903852 387.5882 at 10iterations 5.809941 130.6954 at 20iterations 3.402769 67.73356 at 30iterations 1.991175 40.03368 at 40iterations 1.164230 21.92970 at 50iterations 0.6795893 13.30372 at 60iterations 0.3961495 7.788778 at 70iterations 0.2306371 4.312665 at 80iterations 0.1345297 2.491722 at 90iterations 7.8357100E-02 1.481754 at 100iterations 4.5811865E-02 0.9210653 at 110iterations 2.6763290E-02 0.5520191 at 120iterations 1.5749289E-02 0.2960110 at 130iterations 9.3919858E-03 0.1764698 at 140iterations 5.6956792E-03 0.1158867 at 150iterations 3.5689138E-03 6.8199158E-02 at 160iterations 2.3514158E-03 4.2146683E-02 at 170iterations 1.6286790E-03 2.9962540E-02 at 180iterations finished qdiffx linear iterations at : 15:35:11 total time elapsed so far: 14.59000 # loops : 180 mean,max change (kT/e) : 1.6286790E-03 2.9962540E-02 energy calculations done at 14.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.71000 DelPhi exited at 15:35:11 14.714u 0.293s 0:22.53 66.5% 0+0k 0+0io 0pf+0w