Tue Oct 11 07:33:27 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 Tue Oct 11 2011 at 07:33:27 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3235 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 0.5836927 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): 0.2440000 48.63400 ymin,ymax (A): -8.307000 49.06300 zmin,zma (A): 1.020000 62.01100 x,y,z range (A): 48.39000 57.37000 60.99100 scale (grids/A): 0.5836927 object centre (A): 24.43900 20.37800 31.51550 number of atom coordinates read : 3235 total number of charged atoms : 3090 net assigned charge : -2.085990 assigned positive charge : 488.1697 centred at (gu) : 89.61102 89.41139 90.44305 assigned negative charge : -490.2569 centred at (gu) : 89.54469 89.34086 90.39262 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7194 nv = 96 ne = 84 npr = 67237 no. pairs analyzed = 67237 no. exposed pairs = 3747 no. arc points = 25325 no. surface atoms = 1280 nbur = 1955 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 = 1.456000 m= 352 mr = 4207 m= 0 mr = 29 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2300000 number of dielectric boundary points 3310 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2580 ## 284 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9207 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7076844E-09 9.7222808E-10 midg,1,midg; midg,igrid,midg -2.8173968E-09 1.2286886E-09 1,midg,midg; igrid,midg,midg -2.5594822E-09 1.1856897E-09 gauss-seidel spectral radius is 0.9848623 estimated iterations to convergence 67 setup time was (sec) 0.4100000 now iterating at: 07:33:27 rms-change max change #iterations 0.1071393 15.22170 at 10iterations 8.9341616E-03 1.375729 at 20iterations 9.5625408E-04 0.1478233 at 30iterations 2.3792837E-04 4.2609215E-02 at 40iterations 7.9706013E-05 1.4503479E-02 at 50iterations finished qdiffx linear iterations at : 07:33:30 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 7.9706013E-05 1.4503479E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 07:33:31 3.391u 0.183s 0:04.30 83.0% 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 Tue Oct 11 2011 at 07:33:31 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 = 3235 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 1.751078 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): 0.2440000 48.63400 ymin,ymax (A): -8.307000 49.06300 zmin,zma (A): 1.020000 62.01100 x,y,z range (A): 48.39000 57.37000 60.99100 scale (grids/A): 1.751078 object centre (A): 24.43900 20.37800 31.51550 number of atom coordinates read : 3235 total number of charged atoms : 3090 net assigned charge : -2.085990 assigned positive charge : 488.1697 centred at (gu) : 88.83238 88.23312 91.32855 assigned negative charge : -490.2569 centred at (gu) : 88.63370 88.02235 91.17731 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79476 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25325 grid for indexing accessible points = 1.400000 m= 28272 mr = 57198 m= 3464 mr = 21328 m= 121 mr = 2124 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1416 time to turn everything in is 0.3700000 number of dielectric boundary points 30653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 226 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 23973 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) : 0.5836927 object centre at (A) : 24.43900 20.37800 31.51550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4699453E-02 -2.8029203E-03 midg,1,midg; midg,igrid,midg -1.8432761E-02 2.9916572E-03 1,midg,midg; igrid,midg,midg -1.1090082E-02 4.1314727E-03 gauss-seidel spectral radius is 0.9984488 estimated iterations to convergence 201 setup time was (sec) 0.6000000 now iterating at: 07:33:32 rms-change max change #iterations 4.077128 201.0091 at 10iterations 1.817211 72.62149 at 20iterations 0.8135411 27.08407 at 30iterations 0.3628604 11.10453 at 40iterations 0.1628528 5.440241 at 50iterations 7.2844759E-02 2.469173 at 60iterations 3.2645814E-02 1.096886 at 70iterations 1.4697765E-02 0.4812469 at 80iterations 6.6761361E-03 0.2419548 at 90iterations 3.0871572E-03 9.7003937E-02 at 100iterations 1.4934486E-03 5.2581787E-02 at 110iterations 7.6866784E-04 2.9743433E-02 at 120iterations finished qdiffx linear iterations at : 07:33:39 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 7.6866784E-04 2.9743433E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.730000 DelPhi exited at 07:33:40 7.728u 0.213s 0:08.47 93.6% 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 Tue Oct 11 2011 at 07:33:40 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 = 3235 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 2.626617 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): 0.2440000 48.63400 ymin,ymax (A): -8.307000 49.06300 zmin,zma (A): 1.020000 62.01100 x,y,z range (A): 48.39000 57.37000 60.99100 scale (grids/A): 2.626617 object centre (A): 24.43900 20.37800 31.51550 number of atom coordinates read : 3235 total number of charged atoms : 3090 net assigned charge : -2.085990 assigned positive charge : 488.1697 centred at (gu) : 88.24828 87.34959 91.99248 assigned negative charge : -490.2569 centred at (gu) : 87.95040 87.03329 91.76585 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 184517 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25325 grid for indexing accessible points = 1.400000 m= 94206 mr = 138453 m= 30847 mr = 78575 m= 5741 mr = 24995 m= 533 mr = 4284 m= 7 mr = 326 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 4592 time to turn everything in is 0.9700000 number of dielectric boundary points 69218 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 24711 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) : 1.751078 object centre at (A) : 24.43900 20.37800 31.51550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3845797 -0.2118981 midg,1,midg; midg,igrid,midg -0.3786384 -4.7697537E-03 1,midg,midg; igrid,midg,midg -0.1295799 6.0051110E-02 gauss-seidel spectral radius is 0.9992129 estimated iterations to convergence 281 setup time was (sec) 1.200000 now iterating at: 07:33:41 rms-change max change #iterations 9.967113 262.3259 at 10iterations 5.698144 135.2502 at 20iterations 3.243969 69.26559 at 30iterations 1.849629 36.52103 at 40iterations 1.052177 19.08353 at 50iterations 0.5945045 11.38680 at 60iterations 0.3383113 6.018311 at 70iterations 0.1913228 3.603817 at 80iterations 0.1082992 2.027473 at 90iterations 6.1165139E-02 1.322655 at 100iterations 3.4565784E-02 0.6423950 at 110iterations 1.9587193E-02 0.3600578 at 120iterations 1.1122581E-02 0.2310410 at 130iterations 6.3236575E-03 0.1136112 at 140iterations 3.6240236E-03 7.1566582E-02 at 150iterations 2.1070009E-03 4.1503906E-02 at 160iterations 1.2590538E-03 2.5321960E-02 at 170iterations 7.8018499E-04 1.4997482E-02 at 180iterations finished qdiffx linear iterations at : 07:33:52 total time elapsed so far: 12.41000 # loops : 180 mean,max change (kT/e) : 7.8018499E-04 1.4997482E-02 energy calculations done at 12.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.54000 DelPhi exited at 07:33:53 12.539u 0.220s 0:13.43 94.9% 0+0k 0+0io 0pf+0w