Mon Oct 10 14:24:41 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 Mon Oct 10 2011 at 14:24:41 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2396 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: 0.6043527 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): -24.06900 34.83700 ymin,ymax (A): -14.55000 37.17600 zmin,zma (A): -23.08400 26.32500 x,y,z range (A): 58.90600 51.72600 49.40900 scale (grids/A): 0.6043527 object centre (A): 5.384001 11.31300 1.620501 number of atom coordinates read : 2396 total number of charged atoms : 2239 net assigned charge : -0.9999940 assigned positive charge : 351.8622 centred at (gu) : 90.24200 89.84587 90.35262 assigned negative charge : -352.8625 centred at (gu) : 90.12640 89.90901 90.49271 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5953 nv = 96 ne = 84 npr = 47646 no. pairs analyzed = 47646 no. exposed pairs = 3321 no. arc points = 23142 no. surface atoms = 1117 nbur = 1279 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 275 mr = 2962 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2322 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7282 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3802957E-09 -6.3793730E-09 midg,1,midg; midg,igrid,midg 1.9676918E-09 -2.7944882E-09 1,midg,midg; igrid,midg,midg -4.6615805E-09 4.0704702E-09 gauss-seidel spectral radius is 0.9858190 estimated iterations to convergence 69 setup time was (sec) 0.7000000 now iterating at: 14:24:42 rms-change max change #iterations 0.1053802 17.25924 at 10iterations 8.8932440E-03 1.496620 at 20iterations 7.7186699E-04 0.1320744 at 30iterations 6.4988628E-05 1.1604786E-02 at 40iterations 5.6571898E-06 9.1171265E-04 at 50iterations finished qdiffx linear iterations at : 14:24:46 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 5.6571898E-06 9.1171265E-04 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 14:24:47 4.623u 0.420s 0:05.69 88.5% 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 Mon Oct 10 2011 at 14:24:47 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2396 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: 1.813058 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): -24.06900 34.83700 ymin,ymax (A): -14.55000 37.17600 zmin,zma (A): -23.08400 26.32500 x,y,z range (A): 58.90600 51.72600 49.40900 scale (grids/A): 1.813058 object centre (A): 5.384001 11.31300 1.620501 number of atom coordinates read : 2396 total number of charged atoms : 2239 net assigned charge : -0.9999940 assigned positive charge : 351.8622 centred at (gu) : 90.72551 89.53709 91.05739 assigned negative charge : -352.8625 centred at (gu) : 90.37891 89.72681 91.47786 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 64976 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23142 grid for indexing accessible points = 1.400000 m= 20910 mr = 43038 m= 2542 mr = 14287 m= 103 mr = 1200 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 29991 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 204 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 17541 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) : 0.6043527 object centre at (A) : 5.384001 11.31300 1.620501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2461017E-03 -1.7155187E-02 midg,1,midg; midg,igrid,midg 3.9097676E-03 -9.7750481E-03 1,midg,midg; igrid,midg,midg 3.8385508E-03 1.0087069E-03 gauss-seidel spectral radius is 0.9984854 estimated iterations to convergence 204 setup time was (sec) 1.000000 now iterating at: 14:24:48 rms-change max change #iterations 3.678333 167.9685 at 10iterations 1.645148 73.52032 at 20iterations 0.7403353 26.74374 at 30iterations 0.3311241 11.21271 at 40iterations 0.1491479 5.457269 at 50iterations 6.7219391E-02 2.602036 at 60iterations 3.0106843E-02 0.9760618 at 70iterations 1.3537739E-02 0.4715271 at 80iterations 6.0513266E-03 0.2379932 at 90iterations 2.7239439E-03 9.7558975E-02 at 100iterations 1.2203150E-03 4.4828534E-02 at 110iterations 5.5245950E-04 2.0057678E-02 at 120iterations finished qdiffx linear iterations at : 14:24:58 total time elapsed so far: 10.50000 # loops : 120 mean,max change (kT/e) : 5.5245950E-04 2.0057678E-02 energy calculations done at 10.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.71000 DelPhi exited at 14:24:58 10.718u 0.476s 0:11.56 96.7% 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 Mon Oct 10 2011 at 14:24:59 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2396 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: 2.719587 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): -24.06900 34.83700 ymin,ymax (A): -14.55000 37.17600 zmin,zma (A): -23.08400 26.32500 x,y,z range (A): 58.90600 51.72600 49.40900 scale (grids/A): 2.719587 object centre (A): 5.384001 11.31300 1.620501 number of atom coordinates read : 2396 total number of charged atoms : 2239 net assigned charge : -0.9999940 assigned positive charge : 351.8622 centred at (gu) : 91.08812 89.30566 91.58601 assigned negative charge : -352.8625 centred at (gu) : 90.56828 89.59012 92.21680 start vw surface at 0.1600000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 150611 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23142 grid for indexing accessible points = 1.400000 m= 70832 mr = 105605 m= 21631 mr = 55492 m= 4036 mr = 16009 m= 394 mr = 2499 m= 25 mr = 199 m= 0 mr = 8 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.750000 number of dielectric boundary points 67717 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 17906 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) : 1.813058 object centre at (A) : 5.384001 11.31300 1.620501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6597459E-02 -0.2424622 midg,1,midg; midg,igrid,midg 6.2833428E-02 -0.1748615 1,midg,midg; igrid,midg,midg 0.1271051 -5.3160194E-02 gauss-seidel spectral radius is 0.9992231 estimated iterations to convergence 283 setup time was (sec) 2.120000 now iterating at: 14:25:01 rms-change max change #iterations 9.008848 309.0834 at 10iterations 5.260423 149.7774 at 20iterations 3.029153 76.54993 at 30iterations 1.743721 43.24631 at 40iterations 1.001050 21.49640 at 50iterations 0.5724711 14.24858 at 60iterations 0.3260314 8.090806 at 70iterations 0.1859248 4.553337 at 80iterations 0.1059249 2.311145 at 90iterations 6.0071241E-02 1.210716 at 100iterations 3.4072548E-02 0.7181625 at 110iterations 1.9355053E-02 0.4117622 at 120iterations 1.0953388E-02 0.2314091 at 130iterations 6.2326761E-03 0.1246223 at 140iterations 3.5292343E-03 8.1297979E-02 at 150iterations 2.0024925E-03 4.0740967E-02 at 160iterations 1.1339342E-03 2.1927118E-02 at 170iterations 6.4176886E-04 1.3659954E-02 at 180iterations finished qdiffx linear iterations at : 14:25:17 total time elapsed so far: 17.68000 # loops : 180 mean,max change (kT/e) : 6.4176886E-04 1.3659954E-02 energy calculations done at 17.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.90000 DelPhi exited at 14:25:17 17.904u 0.475s 0:18.73 98.0% 0+0k 0+0io 0pf+0w