Sat Oct 15 15:09:17 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 15:09:17 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 !!! 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: 0.6387941 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): -46.31100 0.9180000 ymin,ymax (A): -47.32700 1.559000 zmin,zma (A): -9.997001 45.73300 x,y,z range (A): 47.22900 48.88600 55.73000 scale (grids/A): 0.6387941 object centre (A): -22.69650 -22.88400 17.86800 number of atom coordinates read : 2710 total number of charged atoms : 2558 net assigned charge : 3.176013 assigned positive charge : 410.5388 centred at (gu) : 90.04456 90.37112 91.91581 assigned negative charge : -407.3633 centred at (gu) : 89.77506 90.17699 91.84908 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7365 nv = 96 ne = 84 npr = 55465 no. pairs analyzed = 55465 no. exposed pairs = 3281 no. arc points = 22812 no. surface atoms = 1092 nbur = 1618 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 4137 m= 1 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2000000 number of dielectric boundary points 3572 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2269 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8817 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3741491E-09 1.8277234E-08 midg,1,midg; midg,igrid,midg -1.7657978E-08 2.8919168E-08 1,midg,midg; igrid,midg,midg -2.8250074E-08 3.5481030E-08 gauss-seidel spectral radius is 0.9873095 estimated iterations to convergence 73 setup time was (sec) 0.4400000 now iterating at: 15:09:17 rms-change max change #iterations 0.1493247 22.32007 at 10iterations 1.4963614E-02 1.899449 at 20iterations 1.6035354E-03 0.2196560 at 30iterations 2.4841365E-04 3.7544250E-02 at 40iterations 6.5718938E-05 8.3198547E-03 at 50iterations finished qdiffx linear iterations at : 15:09:21 total time elapsed so far: 3.860000 # loops : 50 mean,max change (kT/e) : 6.5718938E-05 8.3198547E-03 energy calculations done at 3.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 15:09:21 4.001u 0.250s 0:04.63 91.7% 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 Sat Oct 15 2011 at 15:09:21 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 !!! 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: 1.916382 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): -46.31100 0.9180000 ymin,ymax (A): -47.32700 1.559000 zmin,zma (A): -9.997001 45.73300 x,y,z range (A): 47.22900 48.88600 55.73000 scale (grids/A): 1.916382 object centre (A): -22.69650 -22.88400 17.86800 number of atom coordinates read : 2710 total number of charged atoms : 2558 net assigned charge : 3.176013 assigned positive charge : 410.5388 centred at (gu) : 90.13335 91.11285 95.74682 assigned negative charge : -407.3633 centred at (gu) : 89.32472 90.53075 95.54667 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79403 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22812 grid for indexing accessible points = 1.400000 m= 30065 mr = 56130 m= 4927 mr = 22480 m= 327 mr = 3212 m= 7 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 592 time to turn everything in is 0.4200000 number of dielectric boundary points 32791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 167 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 20123 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) : 0.6387941 object centre at (A) : -22.69650 -22.88400 17.86800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6975464E-02 9.9500101E-03 midg,1,midg; midg,igrid,midg -1.0922736E-02 3.6030699E-02 1,midg,midg; igrid,midg,midg -1.6525216E-02 5.3149376E-02 gauss-seidel spectral radius is 0.9986605 estimated iterations to convergence 216 setup time was (sec) 0.6800000 now iterating at: 15:09:22 rms-change max change #iterations 4.433464 179.7104 at 10iterations 2.094919 77.66268 at 20iterations 0.9943737 32.11964 at 30iterations 0.4709117 15.78701 at 40iterations 0.2216671 7.206118 at 50iterations 0.1050076 3.111694 at 60iterations 4.9500596E-02 1.497467 at 70iterations 2.3469090E-02 0.7292547 at 80iterations 1.1077501E-02 0.3474922 at 90iterations 5.2729528E-03 0.1831799 at 100iterations 2.5082261E-03 7.5413704E-02 at 110iterations 1.2008402E-03 3.8974762E-02 at 120iterations finished qdiffx linear iterations at : 15:09:30 total time elapsed so far: 8.580000 # loops : 120 mean,max change (kT/e) : 1.2008402E-03 3.8974762E-02 energy calculations done at 8.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.710000 DelPhi exited at 15:09:31 8.715u 0.294s 0:09.40 95.7% 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 Sat Oct 15 2011 at 15:09:31 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2710 !!! 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: 2.874574 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): -46.31100 0.9180000 ymin,ymax (A): -47.32700 1.559000 zmin,zma (A): -9.997001 45.73300 x,y,z range (A): 47.22900 48.88600 55.73000 scale (grids/A): 2.874574 object centre (A): -22.69650 -22.88400 17.86800 number of atom coordinates read : 2710 total number of charged atoms : 2558 net assigned charge : 3.176013 assigned positive charge : 410.5388 centred at (gu) : 90.19998 91.66907 98.62012 assigned negative charge : -407.3633 centred at (gu) : 88.98721 90.79600 98.31992 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 183110 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22812 grid for indexing accessible points = 1.400000 m= 96055 mr = 135123 m= 36161 mr = 79527 m= 9066 mr = 29525 m= 1414 mr = 6891 m= 80 mr = 935 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 1855 time to turn everything in is 1.040000 number of dielectric boundary points 73850 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 20456 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) : 1.916382 object centre at (A) : -22.69650 -22.88400 17.86800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3416086 0.3279260 midg,1,midg; midg,igrid,midg -0.1446093 0.4257476 1,midg,midg; igrid,midg,midg -0.1305838 0.4470341 gauss-seidel spectral radius is 0.9992633 estimated iterations to convergence 291 setup time was (sec) 1.310000 now iterating at: 15:09:32 rms-change max change #iterations 10.39887 436.9079 at 10iterations 6.121222 136.7845 at 20iterations 3.570793 74.66199 at 30iterations 2.080177 40.97460 at 40iterations 1.209477 25.12057 at 50iterations 0.7022384 12.90395 at 60iterations 0.4066105 7.572498 at 70iterations 0.2353709 4.358953 at 80iterations 0.1363029 2.554312 at 90iterations 7.8696959E-02 1.416376 at 100iterations 4.5474935E-02 0.8029213 at 110iterations 2.6376624E-02 0.4435768 at 120iterations 1.5294604E-02 0.2868118 at 130iterations 8.8564744E-03 0.1468887 at 140iterations 5.1742224E-03 9.4313383E-02 at 150iterations 3.0563378E-03 6.0108185E-02 at 160iterations 1.8404734E-03 3.3344269E-02 at 170iterations 1.1350058E-03 2.0912170E-02 at 180iterations finished qdiffx linear iterations at : 15:09:44 total time elapsed so far: 13.37000 # loops : 180 mean,max change (kT/e) : 1.1350058E-03 2.0912170E-02 energy calculations done at 13.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.50000 DelPhi exited at 15:09:45 13.499u 0.250s 0:14.07 97.6% 0+0k 0+0io 0pf+0w