Sun Oct 9 06:02:21 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 Sun Oct 9 2011 at 06:02:21 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1747 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIR 132 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6893747 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): 15.64900 67.29000 ymin,ymax (A): 26.72900 77.63700 zmin,zma (A): 47.73500 89.16800 x,y,z range (A): 51.64100 50.90800 41.43300 scale (grids/A): 0.6893747 object centre (A): 41.46950 52.18300 68.45150 number of atom coordinates read : 1747 total number of charged atoms : 1602 net assigned charge : -6.079988 assigned positive charge : 266.9612 centred at (gu) : 90.69395 91.41274 90.65394 assigned negative charge : -273.0412 centred at (gu) : 90.78873 91.86528 90.72495 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5673 nv = 96 ne = 84 npr = 35855 no. pairs analyzed = 35855 no. exposed pairs = 2255 no. arc points = 15844 no. surface atoms = 756 nbur = 991 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 3100 m= 3 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.2400000 number of dielectric boundary points 2861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1464 ## 133 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6372 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.1318588E-09 -5.7610997E-08 midg,1,midg; midg,igrid,midg 6.9415037E-08 -2.2062039E-07 1,midg,midg; igrid,midg,midg -3.2915985E-09 -6.6009122E-08 gauss-seidel spectral radius is 0.9890122 estimated iterations to convergence 78 setup time was (sec) 0.5000000 now iterating at: 06:02:22 rms-change max change #iterations 0.1692242 28.92605 at 10iterations 1.9671779E-02 3.096983 at 20iterations 2.2615336E-03 0.3110611 at 30iterations 2.5974924E-04 3.8047791E-02 at 40iterations 3.0355590E-05 4.6825409E-03 at 50iterations finished qdiffx linear iterations at : 06:02:24 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 3.0355590E-05 4.6825409E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 06:02:25 3.479u 0.192s 0:03.92 93.3% 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 Sun Oct 9 2011 at 06:02:25 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1747 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIR 132 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.068124 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): 15.64900 67.29000 ymin,ymax (A): 26.72900 77.63700 zmin,zma (A): 47.73500 89.16800 x,y,z range (A): 51.64100 50.90800 41.43300 scale (grids/A): 2.068124 object centre (A): 41.46950 52.18300 68.45150 number of atom coordinates read : 1747 total number of charged atoms : 1602 net assigned charge : -6.079988 assigned positive charge : 266.9612 centred at (gu) : 92.08212 94.23808 91.96166 assigned negative charge : -273.0412 centred at (gu) : 92.36639 95.59583 92.17498 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 60055 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15844 grid for indexing accessible points = 1.400000 m= 22957 mr = 40679 m= 4427 mr = 17453 m= 385 mr = 3041 m= 13 mr = 224 m= 0 mr = 3 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 762 time to turn everything in is 0.5000000 number of dielectric boundary points 26437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 12718 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) : 0.6893747 object centre at (A) : 41.46950 52.18300 68.45150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4636705E-03 -3.3343453E-02 midg,1,midg; midg,igrid,midg 6.7531012E-02 -7.4224368E-02 1,midg,midg; igrid,midg,midg -2.5839640E-02 -5.6497734E-02 gauss-seidel spectral radius is 0.9987468 estimated iterations to convergence 224 setup time was (sec) 0.8100000 now iterating at: 06:02:26 rms-change max change #iterations 4.143887 200.7503 at 10iterations 2.002709 72.93120 at 20iterations 0.9660944 35.99950 at 30iterations 0.4674174 15.10889 at 40iterations 0.2252913 7.151664 at 50iterations 0.1088413 4.128738 at 60iterations 5.2644886E-02 1.790694 at 70iterations 2.5501695E-02 0.8595314 at 80iterations 1.2338736E-02 0.4423332 at 90iterations 5.9499899E-03 0.2275677 at 100iterations 2.8789502E-03 9.4661713E-02 at 110iterations 1.3880993E-03 5.0020456E-02 at 120iterations finished qdiffx linear iterations at : 06:02:33 total time elapsed so far: 7.670000 # loops : 120 mean,max change (kT/e) : 1.3880993E-03 5.0020456E-02 energy calculations done at 7.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 06:02:33 7.862u 0.224s 0:08.34 96.8% 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 Sun Oct 9 2011 at 06:02:33 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1747 !!! WARNING: GLM 50 has a net charge of -0.0940 !!! WARNING: HIR 132 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: 3.102186 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): 15.64900 67.29000 ymin,ymax (A): 26.72900 77.63700 zmin,zma (A): 47.73500 89.16800 x,y,z range (A): 51.64100 50.90800 41.43300 scale (grids/A): 3.102186 object centre (A): 41.46950 52.18300 68.45150 number of atom coordinates read : 1747 total number of charged atoms : 1602 net assigned charge : -6.079988 assigned positive charge : 266.9612 centred at (gu) : 93.12325 96.35724 92.94261 assigned negative charge : -273.0412 centred at (gu) : 93.54959 98.39373 93.26256 start vw surface at 0.1300000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 138584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15844 grid for indexing accessible points = 1.400000 m= 71521 mr = 98498 m= 29194 mr = 59128 m= 8341 mr = 24242 m= 1564 mr = 6605 m= 205 mr = 1194 m= 12 mr = 151 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 2481 time to turn everything in is 1.510000 number of dielectric boundary points 59599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 12816 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) : 2.068124 object centre at (A) : 41.46950 52.18300 68.45150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1875182 -0.2451950 midg,1,midg; midg,igrid,midg 0.6255031 -0.5322604 1,midg,midg; igrid,midg,midg -0.2769557 -0.6183355 gauss-seidel spectral radius is 0.9992756 estimated iterations to convergence 293 setup time was (sec) 1.850000 now iterating at: 06:02:35 rms-change max change #iterations 9.394996 352.4795 at 10iterations 5.430343 119.3827 at 20iterations 3.153118 61.40746 at 30iterations 1.822323 40.81978 at 40iterations 1.053962 20.67139 at 50iterations 0.6078373 12.58754 at 60iterations 0.3515643 6.603050 at 70iterations 0.2027678 3.989099 at 80iterations 0.1173031 2.182055 at 90iterations 6.7605495E-02 1.322816 at 100iterations 3.9072305E-02 0.7562103 at 110iterations 2.2502000E-02 0.4450073 at 120iterations 1.2992285E-02 0.2597294 at 130iterations 7.4935998E-03 0.1485395 at 140iterations 4.3228786E-03 8.1912994E-02 at 150iterations 2.4907622E-03 4.7357559E-02 at 160iterations 1.4365234E-03 3.1082869E-02 at 170iterations 8.3045400E-04 1.6253471E-02 at 180iterations finished qdiffx linear iterations at : 06:02:48 total time elapsed so far: 14.02000 # loops : 180 mean,max change (kT/e) : 8.3045400E-04 1.6253471E-02 energy calculations done at 14.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.21000 DelPhi exited at 06:02:48 14.209u 0.219s 0:14.68 98.1% 0+0k 0+0io 0pf+0w