Sat Oct 15 15:07:40 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 15:07:40 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2851 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.6287864 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): -12.16400 36.64400 ymin,ymax (A): 3.357000 51.96000 zmin,zma (A): -11.14900 45.46800 x,y,z range (A): 48.80800 48.60300 56.61700 scale (grids/A): 0.6287864 object centre (A): 12.24000 27.65850 17.15950 number of atom coordinates read : 2851 total number of charged atoms : 2692 net assigned charge : 2.451019 assigned positive charge : 435.4026 centred at (gu) : 90.28008 90.70021 91.78456 assigned negative charge : -432.9521 centred at (gu) : 90.08296 90.56594 91.73237 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7516 nv = 96 ne = 84 npr = 57592 no. pairs analyzed = 57592 no. exposed pairs = 3467 no. arc points = 23797 no. surface atoms = 1174 nbur = 1677 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 4273 m= 1 mr = 23 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 0.2200000 number of dielectric boundary points 3589 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2379 ## 247 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 9072 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7586109E-09 1.0759272E-08 midg,1,midg; midg,igrid,midg -9.0778913E-09 1.7395580E-08 1,midg,midg; igrid,midg,midg -1.5795147E-08 2.1980341E-08 gauss-seidel spectral radius is 0.9869165 estimated iterations to convergence 72 setup time was (sec) 0.4500000 now iterating at: 15:07:40 rms-change max change #iterations 0.1447672 18.73135 at 10iterations 1.4439239E-02 1.982506 at 20iterations 1.4948749E-03 0.2184048 at 30iterations 2.0479874E-04 2.7801514E-02 at 40iterations 5.1378505E-05 7.2097778E-03 at 50iterations finished qdiffx linear iterations at : 15:07:44 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 5.1378505E-05 7.2097778E-03 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.900000 DelPhi exited at 15:07:44 3.905u 0.253s 0:04.43 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 Sat Oct 15 2011 at 15:07:44 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2851 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 1.886359 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): -12.16400 36.64400 ymin,ymax (A): 3.357000 51.96000 zmin,zma (A): -11.14900 45.46800 x,y,z range (A): 48.80800 48.60300 56.61700 scale (grids/A): 1.886359 object centre (A): 12.24000 27.65850 17.15950 number of atom coordinates read : 2851 total number of charged atoms : 2692 net assigned charge : 2.451019 assigned positive charge : 435.4026 centred at (gu) : 90.83963 92.09977 95.35329 assigned negative charge : -432.9521 centred at (gu) : 90.24853 91.69732 95.19678 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80957 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23797 grid for indexing accessible points = 1.400000 m= 29451 mr = 57295 m= 4294 mr = 21919 m= 218 mr = 2478 m= 5 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 187 time to turn everything in is 0.4200000 number of dielectric boundary points 33162 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 21106 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) : 0.6287864 object centre at (A) : 12.24000 27.65850 17.15950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5741834E-02 1.0779677E-02 midg,1,midg; midg,igrid,midg -1.6654171E-02 1.4069672E-04 1,midg,midg; igrid,midg,midg -7.7847238E-03 5.0312378E-02 gauss-seidel spectral radius is 0.9986324 estimated iterations to convergence 214 setup time was (sec) 0.6800000 now iterating at: 15:07:45 rms-change max change #iterations 4.501546 179.8473 at 10iterations 2.102565 68.88650 at 20iterations 0.9883694 31.66439 at 30iterations 0.4631148 14.75602 at 40iterations 0.2178909 8.398392 at 50iterations 0.1021903 3.007481 at 60iterations 4.7842339E-02 1.582527 at 70iterations 2.2443488E-02 0.7293205 at 80iterations 1.0551519E-02 0.3132191 at 90iterations 4.9292902E-03 0.1480918 at 100iterations 2.3207832E-03 6.6200256E-02 at 110iterations 1.0910056E-03 3.5890579E-02 at 120iterations finished qdiffx linear iterations at : 15:07:53 total time elapsed so far: 8.940000 # loops : 120 mean,max change (kT/e) : 1.0910056E-03 3.5890579E-02 energy calculations done at 8.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.080000 DelPhi exited at 15:07:54 9.080u 0.283s 0:09.73 96.1% 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 15:07:54 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2851 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: GLV 97 has a net charge of -0.5880 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.829539 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): -12.16400 36.64400 ymin,ymax (A): 3.357000 51.96000 zmin,zma (A): -11.14900 45.46800 x,y,z range (A): 48.80800 48.60300 56.61700 scale (grids/A): 2.829539 object centre (A): 12.24000 27.65850 17.15950 number of atom coordinates read : 2851 total number of charged atoms : 2692 net assigned charge : 2.451019 assigned positive charge : 435.4026 centred at (gu) : 91.25916 93.14943 98.02988 assigned negative charge : -432.9521 centred at (gu) : 90.37280 92.54580 97.79509 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 187377 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23797 grid for indexing accessible points = 1.400000 m= 96232 mr = 138662 m= 33983 mr = 79434 m= 7572 mr = 27205 m= 958 mr = 5428 m= 72 mr = 589 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 587 time to turn everything in is 1.100000 number of dielectric boundary points 74853 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 21534 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) : 1.886359 object centre at (A) : 12.24000 27.65850 17.15950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3068382 0.2220182 midg,1,midg; midg,igrid,midg -0.2066477 -3.7770234E-02 1,midg,midg; igrid,midg,midg -4.8995353E-02 0.4664518 gauss-seidel spectral radius is 0.9992564 estimated iterations to convergence 289 setup time was (sec) 1.400000 now iterating at: 15:07:56 rms-change max change #iterations 10.51144 402.2343 at 10iterations 6.152740 139.1593 at 20iterations 3.581479 74.78847 at 30iterations 2.077933 45.16948 at 40iterations 1.203696 22.93214 at 50iterations 0.6941270 13.46526 at 60iterations 0.4009409 7.241730 at 70iterations 0.2311943 4.385551 at 80iterations 0.1332626 2.427256 at 90iterations 7.6690808E-02 1.408030 at 100iterations 4.4175498E-02 0.7407303 at 110iterations 2.5468955E-02 0.4417877 at 120iterations 1.4634904E-02 0.2557373 at 130iterations 8.4348544E-03 0.1544800 at 140iterations 4.8593301E-03 8.5649490E-02 at 150iterations 2.8119476E-03 5.1645279E-02 at 160iterations 1.6356619E-03 2.7463913E-02 at 170iterations 9.5701945E-04 1.6275406E-02 at 180iterations finished qdiffx linear iterations at : 15:08:09 total time elapsed so far: 14.57000 # loops : 180 mean,max change (kT/e) : 9.5701945E-04 1.6275406E-02 energy calculations done at 14.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.70000 DelPhi exited at 15:08:09 14.701u 0.307s 0:15.29 98.1% 0+0k 0+0io 0pf+0w