Sat Oct 15 12:21:54 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 12:21:54 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4480 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.4404741 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): -2.799000 78.02300 ymin,ymax (A): 0.8119999 66.39700 zmin,zma (A): 175.2530 236.7070 x,y,z range (A): 80.82201 65.58501 61.45401 scale (grids/A): 0.4404741 object centre (A): 37.61200 33.60450 205.9800 number of atom coordinates read : 4480 total number of charged atoms : 4253 net assigned charge : 22.99997 assigned positive charge : 655.9813 centred at (gu) : 85.84609 91.20181 88.77431 assigned negative charge : -632.9860 centred at (gu) : 85.79182 91.17040 88.80490 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5169 nv = 96 ne = 84 npr = 90754 no. pairs analyzed = 90754 no. exposed pairs = 5816 no. arc points = 39911 no. surface atoms = 1979 nbur = 2501 mkacc time = 0.1600000 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 = 1.904000 m= 129 mr = 2429 m= 0 mr = 1 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3298 ## 661 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7033 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5457486E-11 4.5604722E-12 midg,1,midg; midg,igrid,midg 4.5529322E-12 1.5426566E-11 1,midg,midg; igrid,midg,midg 1.6325163E-11 3.6768115E-12 gauss-seidel spectral radius is 0.9736922 estimated iterations to convergence 51 setup time was (sec) 0.4900000 now iterating at: 12:21:55 rms-change max change #iterations 3.0523026E-02 6.317879 at 10iterations 3.0876000E-03 0.5907974 at 20iterations 8.8247715E-04 0.1454821 at 30iterations 2.7108469E-04 4.7209263E-02 at 40iterations 8.4363368E-05 1.5196323E-02 at 50iterations finished qdiffx linear iterations at : 12:21:58 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 8.4363368E-05 1.5196323E-02 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 12:21:58 3.652u 0.182s 0:04.20 91.1% 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 12:21:58 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4480 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.321422 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): -2.799000 78.02300 ymin,ymax (A): 0.8119999 66.39700 zmin,zma (A): 175.2530 236.7070 x,y,z range (A): 80.82201 65.58501 61.45401 scale (grids/A): 1.321422 object centre (A): 37.61200 33.60450 205.9800 number of atom coordinates read : 4480 total number of charged atoms : 4253 net assigned charge : 22.99997 assigned positive charge : 655.9813 centred at (gu) : 77.53658 93.60393 86.32069 assigned negative charge : -632.9860 centred at (gu) : 77.37502 93.51090 86.41455 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 59726 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39911 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 14283 mr = 38879 m= 731 mr = 8642 m= 8 mr = 158 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 143 time to turn everything in is 0.3200000 number of dielectric boundary points 27069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 714 ## 27 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 30009 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) : 0.4404741 object centre at (A) : 37.61200 33.60450 205.9800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5071497E-03 7.9530233E-04 midg,1,midg; midg,igrid,midg 3.1968991E-03 5.7852315E-03 1,midg,midg; igrid,midg,midg 2.6092593E-02 2.7579528E-03 gauss-seidel spectral radius is 0.9973072 estimated iterations to convergence 154 setup time was (sec) 0.5500000 now iterating at: 12:21:59 rms-change max change #iterations 2.466382 128.5016 at 10iterations 0.8482566 32.32069 at 20iterations 0.2952586 12.33639 at 30iterations 0.1016999 4.301300 at 40iterations 3.5488300E-02 1.421030 at 50iterations 1.2494179E-02 0.5208778 at 60iterations 4.6032942E-03 0.1926770 at 70iterations 1.8820352E-03 7.3835373E-02 at 80iterations 9.2341739E-04 3.7405014E-02 at 90iterations 5.5135868E-04 2.1269798E-02 at 100iterations 3.6135069E-04 1.3301849E-02 at 110iterations 2.4653386E-04 9.3984604E-03 at 120iterations finished qdiffx linear iterations at : 12:22:06 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 2.4653386E-04 9.3984604E-03 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 12:22:07 7.863u 0.210s 0:08.50 94.9% 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 12:22:07 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4480 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.982133 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): -2.799000 78.02300 ymin,ymax (A): 0.8119999 66.39700 zmin,zma (A): 175.2530 236.7070 x,y,z range (A): 80.82201 65.58501 61.45401 scale (grids/A): 1.982133 object centre (A): 37.61200 33.60450 205.9800 number of atom coordinates read : 4480 total number of charged atoms : 4253 net assigned charge : 22.99997 assigned positive charge : 655.9813 centred at (gu) : 71.30451 95.40559 84.48078 assigned negative charge : -632.9860 centred at (gu) : 71.06240 95.26622 84.62175 start vw surface at 0.1200000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 140067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39911 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 54507 mr = 97270 m= 10558 mr = 40415 m= 831 mr = 6865 m= 13 mr = 347 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 492 time to turn everything in is 0.7500000 number of dielectric boundary points 61080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 33602 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) : 1.321422 object centre at (A) : 37.61200 33.60450 205.9800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1153667 1.4447362E-02 midg,1,midg; midg,igrid,midg 8.4857158E-02 0.1381708 1,midg,midg; igrid,midg,midg 0.6402843 3.9398015E-02 gauss-seidel spectral radius is 0.9988673 estimated iterations to convergence 235 setup time was (sec) 0.9900000 now iterating at: 12:22:08 rms-change max change #iterations 7.311947 239.0552 at 10iterations 3.779039 97.17434 at 20iterations 1.949543 55.44261 at 30iterations 0.9958221 23.41729 at 40iterations 0.5077123 12.53404 at 50iterations 0.2589828 6.622923 at 60iterations 0.1312739 3.117443 at 70iterations 6.6564813E-02 1.693159 at 80iterations 3.3673741E-02 0.8341160 at 90iterations 1.7088998E-02 0.4020104 at 100iterations 8.6930329E-03 0.2016134 at 110iterations 4.4544144E-03 9.8867416E-02 at 120iterations 2.3177967E-03 5.3819656E-02 at 130iterations 1.2538745E-03 3.1603813E-02 at 140iterations 7.2011782E-04 1.7125368E-02 at 150iterations 4.5209168E-04 1.1560440E-02 at 160iterations 3.0961548E-04 7.4920654E-03 at 170iterations 2.2666709E-04 5.4597855E-03 at 180iterations finished qdiffx linear iterations at : 12:22:19 total time elapsed so far: 12.26000 # loops : 180 mean,max change (kT/e) : 2.2666709E-04 5.4597855E-03 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.39000 DelPhi exited at 12:22:20 12.396u 0.219s 0:13.05 96.5% 0+0k 0+0io 0pf+0w