Mon Oct 10 10:25:13 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 10:25:13 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2769 !!! WARNING: HIT 236 has a net charge of 0.5140 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: 0.5652768 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): -20.10400 42.87400 ymin,ymax (A): -9.075000 45.52100 zmin,zma (A): -1.639000 51.51000 x,y,z range (A): 62.97800 54.59600 53.14900 scale (grids/A): 0.5652768 object centre (A): 11.38500 18.22300 24.93550 number of atom coordinates read : 2769 total number of charged atoms : 2621 net assigned charge : 8.014016 assigned positive charge : 406.3740 centred at (gu) : 91.00197 90.38734 86.53023 assigned negative charge : -398.3605 centred at (gu) : 91.16237 90.37011 86.44512 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5882 nv = 96 ne = 84 npr = 53645 no. pairs analyzed = 53645 no. exposed pairs = 4219 no. arc points = 30488 no. surface atoms = 1401 nbur = 1368 mkacc time = 0.1000000 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= 277 mr = 2563 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2975 ## 340 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7566 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6088454E-11 9.2126379E-10 midg,1,midg; midg,igrid,midg 8.0286161E-10 1.4042680E-09 1,midg,midg; igrid,midg,midg 2.3055959E-09 -1.0903680E-09 gauss-seidel spectral radius is 0.9838535 estimated iterations to convergence 65 setup time was (sec) 0.4100000 now iterating at: 10:25:14 rms-change max change #iterations 8.4120952E-02 15.48924 at 10iterations 6.0556894E-03 1.069798 at 20iterations 4.8175809E-04 9.4309807E-02 at 30iterations 5.8324898E-05 1.2768745E-02 at 40iterations 1.2001030E-05 3.0126572E-03 at 50iterations finished qdiffx linear iterations at : 10:25:16 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.2001030E-05 3.0126572E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 10:25:17 3.458u 0.202s 0:04.08 89.4% 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 10:25:17 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2769 !!! WARNING: HIT 236 has a net charge of 0.5140 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: 1.695830 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): -20.10400 42.87400 ymin,ymax (A): -9.075000 45.52100 zmin,zma (A): -1.639000 51.51000 x,y,z range (A): 62.97800 54.59600 53.14900 scale (grids/A): 1.695830 object centre (A): 11.38500 18.22300 24.93550 number of atom coordinates read : 2769 total number of charged atoms : 2621 net assigned charge : 8.014016 assigned positive charge : 406.3740 centred at (gu) : 93.00552 91.16157 79.59013 assigned negative charge : -398.3605 centred at (gu) : 93.48711 91.10986 79.33504 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 63594 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30488 grid for indexing accessible points = 1.400000 m= 19650 mr = 38592 m= 2237 mr = 12444 m= 74 mr = 957 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 33560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 276 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20253 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) : 0.5652768 object centre at (A) : 11.38500 18.22300 24.93550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0523535E-03 5.7681021E-03 midg,1,midg; midg,igrid,midg 1.4904594E-02 1.3236441E-02 1,midg,midg; igrid,midg,midg 1.3532503E-02 -1.6861232E-02 gauss-seidel spectral radius is 0.9983141 estimated iterations to convergence 193 setup time was (sec) 0.5600000 now iterating at: 10:25:18 rms-change max change #iterations 3.416513 158.1469 at 10iterations 1.461600 65.74046 at 20iterations 0.6263131 26.11046 at 30iterations 0.2676058 9.900654 at 40iterations 0.1145763 4.226160 at 50iterations 4.9284812E-02 1.856036 at 60iterations 2.1118220E-02 0.7926350 at 70iterations 9.0813916E-03 0.3299103 at 80iterations 3.9062023E-03 0.1467748 at 90iterations 1.6756429E-03 6.2917709E-02 at 100iterations 7.2749483E-04 2.6477814E-02 at 110iterations 3.1605377E-04 1.1775017E-02 at 120iterations finished qdiffx linear iterations at : 10:25:26 total time elapsed so far: 8.390000 # loops : 120 mean,max change (kT/e) : 3.1605377E-04 1.1775017E-02 energy calculations done at 8.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.520000 DelPhi exited at 10:25:27 8.525u 0.250s 0:09.66 90.7% 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 10:25:27 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2769 !!! WARNING: HIT 236 has a net charge of 0.5140 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: 2.543746 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): -20.10400 42.87400 ymin,ymax (A): -9.075000 45.52100 zmin,zma (A): -1.639000 51.51000 x,y,z range (A): 62.97800 54.59600 53.14900 scale (grids/A): 2.543746 object centre (A): 11.38500 18.22300 24.93550 number of atom coordinates read : 2769 total number of charged atoms : 2621 net assigned charge : 8.014016 assigned positive charge : 406.3740 centred at (gu) : 94.50828 91.74239 74.38508 assigned negative charge : -398.3605 centred at (gu) : 95.23060 91.66473 74.00237 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 146934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30488 grid for indexing accessible points = 1.400000 m= 65494 mr = 95352 m= 19825 mr = 48657 m= 3373 mr = 13936 m= 279 mr = 2084 m= 7 mr = 87 m= 0 mr = 1 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7900000 number of dielectric boundary points 75795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 20955 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) : 1.695830 object centre at (A) : 11.38500 18.22300 24.93550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4639297E-02 6.3925862E-02 midg,1,midg; midg,igrid,midg 0.2594247 0.1744718 1,midg,midg; igrid,midg,midg 0.1032573 -0.6156520 gauss-seidel spectral radius is 0.9991845 estimated iterations to convergence 277 setup time was (sec) 1.030000 now iterating at: 10:25:28 rms-change max change #iterations 8.973912 352.7245 at 10iterations 5.247127 156.2516 at 20iterations 3.019644 82.54974 at 30iterations 1.728859 43.93968 at 40iterations 0.9820651 25.59854 at 50iterations 0.5557781 13.44934 at 60iterations 0.3135666 7.747411 at 70iterations 0.1766180 4.395584 at 80iterations 9.9183917E-02 2.358335 at 90iterations 5.5760350E-02 1.304976 at 100iterations 3.1261623E-02 0.7919264 at 110iterations 1.7500581E-02 0.3875580 at 120iterations 9.7962143E-03 0.2181821 at 130iterations 5.4731783E-03 0.1194229 at 140iterations 3.0636315E-03 7.5212479E-02 at 150iterations 1.7146786E-03 3.5514832E-02 at 160iterations 9.5433294E-04 2.1745682E-02 at 170iterations 5.3606305E-04 1.2111664E-02 at 180iterations finished qdiffx linear iterations at : 10:25:39 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 5.3606305E-04 1.2111664E-02 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 10:25:40 12.426u 0.234s 0:13.16 96.1% 0+0k 0+0io 0pf+0w