Fri Mar 2 14:30:01 PST 2012 #!/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_thinner.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 Fri Mar 2 2012 at 14:30:01 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: 17 atomic charges read from file fort.12 # of charge parameter records: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2766 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: 0.5725774 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 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): -13.88300 48.29200 ymin,ymax (A): -27.17500 25.34100 zmin,zma (A): -29.86900 30.00800 x,y,z range (A): 62.17500 52.51600 59.87700 scale (grids/A): 0.5725774 object centre (A): 17.20450 -0.9169998 6.9499969E-02 number of atom coordinates read : 2766 total number of charged atoms : 2629 net assigned charge : 6.000009 assigned positive charge : 395.1085 centred at (gu) : 89.48950 89.73661 91.14871 assigned negative charge : -389.1095 centred at (gu) : 89.87074 90.05724 91.02950 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5926 nv = 96 ne = 84 npr = 59367 no. pairs analyzed = 59367 no. exposed pairs = 3925 no. arc points = 27488 no. surface atoms = 1330 nbur = 1436 mkacc time = 0.1100000 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 = 1.512000 m= 273 mr = 2541 m= 0 mr = 11 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2799 ## 271 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1554630E-08 8.3693173E-08 midg,1,midg; midg,igrid,midg 1.3942758E-07 -8.2266041E-08 1,midg,midg; igrid,midg,midg 1.6796422E-07 -9.8181516E-08 gauss-seidel spectral radius is 0.9890049 estimated iterations to convergence 78 setup time was (sec) 0.4600000 now iterating at: 14:30:01 rms-change max change #iterations 0.1259350 20.21854 at 10iterations 1.4949827E-02 2.291805 at 20iterations 2.2818544E-03 0.4157867 at 30iterations 5.6810188E-04 0.1112442 at 40iterations 1.8194442E-04 3.7044525E-02 at 50iterations finished qdiffx linear iterations at : 14:30:07 total time elapsed so far: 3.800000 # loops : 50 mean,max change (kT/e) : 1.8194442E-04 3.7044525E-02 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.940000 DelPhi exited at 14:30:07 3.942u 0.259s 0:06.56 63.8% 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 Fri Mar 2 2012 at 14:30:07 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: 17 atomic charges read from file fort.12 # of charge parameter records: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2766 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: 1.717732 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 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): -13.88300 48.29200 ymin,ymax (A): -27.17500 25.34100 zmin,zma (A): -29.86900 30.00800 x,y,z range (A): 62.17500 52.51600 59.87700 scale (grids/A): 1.717732 object centre (A): 17.20450 -0.9169998 6.9499969E-02 number of atom coordinates read : 2766 total number of charged atoms : 2629 net assigned charge : 6.000009 assigned positive charge : 395.1085 centred at (gu) : 88.46775 89.20886 93.44558 assigned negative charge : -389.1095 centred at (gu) : 89.61179 90.17160 93.08803 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 63868 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27488 grid for indexing accessible points = 1.400000 m= 19343 mr = 39276 m= 2544 mr = 11978 m= 96 mr = 1109 m= 1 mr = 18 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 0.3900000 number of dielectric boundary points 33471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 220 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 20388 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) : 0.5725774 object centre at (A) : 17.20450 -0.9169998 6.9499969E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5340653E-03 2.6047343E-02 midg,1,midg; midg,igrid,midg 7.4853055E-02 -2.2406554E-02 1,midg,midg; igrid,midg,midg 8.2309142E-02 -6.7695379E-02 gauss-seidel spectral radius is 0.9987329 estimated iterations to convergence 223 setup time was (sec) 0.6800000 now iterating at: 14:30:08 rms-change max change #iterations 3.909471 188.5655 at 10iterations 1.877796 76.53436 at 20iterations 0.8998827 37.72437 at 30iterations 0.4332979 18.43748 at 40iterations 0.2083713 7.086749 at 50iterations 0.1002347 3.529220 at 60iterations 4.8483148E-02 1.954609 at 70iterations 2.3353923E-02 1.034813 at 80iterations 1.1346764E-02 0.4246330 at 90iterations 5.6145769E-03 0.2124596 at 100iterations 2.8615587E-03 0.1338310 at 110iterations 1.5314088E-03 6.5059662E-02 at 120iterations finished qdiffx linear iterations at : 14:30:25 total time elapsed so far: 9.160000 # loops : 120 mean,max change (kT/e) : 1.5314088E-03 6.5059662E-02 energy calculations done at 9.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.300000 DelPhi exited at 14:30:26 9.301u 0.269s 0:18.48 51.7% 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 Fri Mar 2 2012 at 14:30:26 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: 17 atomic charges read from file fort.12 # of charge parameter records: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2766 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: 2.576598 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.000000 78.00000 ionic strength (M) : 0.1000000 debye length (A) : 9.635460 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): -13.88300 48.29200 ymin,ymax (A): -27.17500 25.34100 zmin,zma (A): -29.86900 30.00800 x,y,z range (A): 62.17500 52.51600 59.87700 scale (grids/A): 2.576598 object centre (A): 17.20450 -0.9169998 6.9499969E-02 number of atom coordinates read : 2766 total number of charged atoms : 2629 net assigned charge : 6.000009 assigned positive charge : 395.1085 centred at (gu) : 87.70139 88.81316 95.16814 assigned negative charge : -389.1095 centred at (gu) : 89.41757 90.25727 94.63197 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 147861 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27488 grid for indexing accessible points = 1.400000 m= 64548 mr = 97499 m= 20387 mr = 47549 m= 4064 mr = 14167 m= 408 mr = 2501 m= 13 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.000000 number of dielectric boundary points 75387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 21019 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) : 1.717732 object centre at (A) : 17.20450 -0.9169998 6.9499969E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7641368E-02 0.2339568 midg,1,midg; midg,igrid,midg 0.5328238 -0.1862056 1,midg,midg; igrid,midg,midg 0.7382113 -0.9139110 gauss-seidel spectral radius is 0.9992788 estimated iterations to convergence 294 setup time was (sec) 1.300000 now iterating at: 14:30:28 rms-change max change #iterations 9.232830 322.8917 at 10iterations 5.473590 157.7299 at 20iterations 3.213040 71.10600 at 30iterations 1.880570 43.66583 at 40iterations 1.096928 24.26659 at 50iterations 0.6381981 15.11252 at 60iterations 0.3707535 8.229822 at 70iterations 0.2151781 4.706946 at 80iterations 0.1249398 2.593002 at 90iterations 7.2352275E-02 1.712578 at 100iterations 4.1826505E-02 0.8530102 at 110iterations 2.4260286E-02 0.5136042 at 120iterations 1.4085594E-02 0.2793503 at 130iterations 8.2272394E-03 0.1675415 at 140iterations 4.8065586E-03 0.1102371 at 150iterations 2.8672714E-03 7.2463989E-02 at 160iterations 1.7501507E-03 3.9039612E-02 at 170iterations 1.1255217E-03 2.7259827E-02 at 180iterations finished qdiffx linear iterations at : 14:30:53 total time elapsed so far: 13.67000 # loops : 180 mean,max change (kT/e) : 1.1255217E-03 2.7259827E-02 energy calculations done at 13.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 14:30:54 13.805u 0.286s 0:28.06 50.1% 0+0k 0+0io 0pf+0w