Sat Oct 15 15:11:23 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 15:11:23 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2722 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6424717 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): -45.98700 0.9400000 ymin,ymax (A): -47.16800 1.579000 zmin,zma (A): -9.662001 45.74900 x,y,z range (A): 46.92700 48.74700 55.41100 scale (grids/A): 0.6424717 object centre (A): -22.52350 -22.79450 18.04350 number of atom coordinates read : 2722 total number of charged atoms : 2570 net assigned charge : 4.176017 assigned positive charge : 414.0029 centred at (gu) : 89.96680 90.32694 91.73969 assigned negative charge : -409.8273 centred at (gu) : 89.68088 90.12310 91.70425 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7490 nv = 96 ne = 84 npr = 55425 no. pairs analyzed = 55425 no. exposed pairs = 3308 no. arc points = 22976 no. surface atoms = 1111 nbur = 1611 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 414 mr = 4244 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2100000 number of dielectric boundary points 3612 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2245 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8982 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2945054E-09 1.6011350E-08 midg,1,midg; midg,igrid,midg -1.9492694E-08 3.4987824E-08 1,midg,midg; igrid,midg,midg -3.2562706E-08 4.2524618E-08 gauss-seidel spectral radius is 0.9874554 estimated iterations to convergence 73 setup time was (sec) 0.4300000 now iterating at: 15:11:24 rms-change max change #iterations 0.1528049 20.37918 at 10iterations 1.5749501E-02 2.368998 at 20iterations 1.6890621E-03 0.2377186 at 30iterations 2.3421062E-04 3.1089783E-02 at 40iterations 5.6826739E-05 8.9550018E-03 at 50iterations finished qdiffx linear iterations at : 15:11:27 total time elapsed so far: 3.700000 # loops : 50 mean,max change (kT/e) : 5.6826739E-05 8.9550018E-03 energy calculations done at 3.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.840000 DelPhi exited at 15:11:28 3.843u 0.221s 0:04.36 93.1% 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 15:11:28 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2722 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.927415 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): -45.98700 0.9400000 ymin,ymax (A): -47.16800 1.579000 zmin,zma (A): -9.662001 45.74900 x,y,z range (A): 46.92700 48.74700 55.41100 scale (grids/A): 1.927415 object centre (A): -22.52350 -22.79450 18.04350 number of atom coordinates read : 2722 total number of charged atoms : 2570 net assigned charge : 4.176017 assigned positive charge : 414.0029 centred at (gu) : 89.89995 90.98054 95.21886 assigned negative charge : -409.8273 centred at (gu) : 89.04236 90.36893 95.11243 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80933 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22976 grid for indexing accessible points = 1.400000 m= 31014 mr = 57243 m= 5232 mr = 23324 m= 326 mr = 3314 m= 9 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 975 time to turn everything in is 0.4200000 number of dielectric boundary points 33507 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 158 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20224 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) : 0.6424717 object centre at (A) : -22.52350 -22.79450 18.04350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.9645244E-02 9.0164077E-03 midg,1,midg; midg,igrid,midg -1.0521138E-02 3.8725574E-02 1,midg,midg; igrid,midg,midg -1.6681340E-02 5.5431500E-02 gauss-seidel spectral radius is 0.9986789 estimated iterations to convergence 218 setup time was (sec) 0.6800000 now iterating at: 15:11:29 rms-change max change #iterations 4.515887 180.6245 at 10iterations 2.145821 79.42487 at 20iterations 1.021556 34.34977 at 30iterations 0.4865165 15.46416 at 40iterations 0.2302553 7.014259 at 50iterations 0.1091903 3.352504 at 60iterations 5.2084811E-02 1.669862 at 70iterations 2.4755776E-02 0.7213898 at 80iterations 1.1787442E-02 0.3283920 at 90iterations 5.6178598E-03 0.1901751 at 100iterations 2.6767084E-03 8.6486816E-02 at 110iterations 1.2886138E-03 3.8002014E-02 at 120iterations finished qdiffx linear iterations at : 15:11:37 total time elapsed so far: 8.760000 # loops : 120 mean,max change (kT/e) : 1.2886138E-03 3.8002014E-02 energy calculations done at 8.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.890000 DelPhi exited at 15:11:37 8.892u 0.262s 0:09.42 97.1% 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 15:11:37 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2722 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.891123 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): -45.98700 0.9400000 ymin,ymax (A): -47.16800 1.579000 zmin,zma (A): -9.662001 45.74900 x,y,z range (A): 46.92700 48.74700 55.41100 scale (grids/A): 2.891123 object centre (A): -22.52350 -22.79450 18.04350 number of atom coordinates read : 2722 total number of charged atoms : 2570 net assigned charge : 4.176017 assigned positive charge : 414.0029 centred at (gu) : 89.84988 91.47073 97.82816 assigned negative charge : -409.8273 centred at (gu) : 88.56355 90.55333 97.66861 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 186870 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22976 grid for indexing accessible points = 1.400000 m= 99034 mr = 138355 m= 37828 mr = 81846 m= 9559 mr = 30801 m= 1350 mr = 7243 m= 93 mr = 861 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 3277 time to turn everything in is 1.130000 number of dielectric boundary points 75588 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.250000 number of grid points assigned charge 20553 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) : 1.927415 object centre at (A) : -22.52350 -22.79450 18.04350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2694269 0.3572748 midg,1,midg; midg,igrid,midg -0.1326253 0.4315866 1,midg,midg; igrid,midg,midg -0.1256499 0.4485002 gauss-seidel spectral radius is 0.9992682 estimated iterations to convergence 292 setup time was (sec) 1.420000 now iterating at: 15:11:39 rms-change max change #iterations 10.52808 336.2776 at 10iterations 6.186209 143.2603 at 20iterations 3.611858 70.74709 at 30iterations 2.110450 47.75897 at 40iterations 1.226465 23.31786 at 50iterations 0.7138122 13.24616 at 60iterations 0.4140721 8.286723 at 70iterations 0.2395598 4.310754 at 80iterations 0.1386728 2.495951 at 90iterations 8.0384120E-02 1.417117 at 100iterations 4.6447080E-02 0.9618425 at 110iterations 2.6950067E-02 0.4844856 at 120iterations 1.5657894E-02 0.2986746 at 130iterations 9.0858173E-03 0.1536865 at 140iterations 5.3007500E-03 8.7248325E-02 at 150iterations 3.1197148E-03 5.3613663E-02 at 160iterations 1.8684509E-03 3.4072876E-02 at 170iterations 1.1471040E-03 2.2476196E-02 at 180iterations finished qdiffx linear iterations at : 15:11:52 total time elapsed so far: 15.02000 # loops : 180 mean,max change (kT/e) : 1.1471040E-03 2.2476196E-02 energy calculations done at 15.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.15000 DelPhi exited at 15:11:53 15.151u 0.285s 0:15.81 97.5% 0+0k 0+0io 0pf+0w