Sat Oct 8 15:47:05 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 8 2011 at 15:47:05 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2300 !!! WARNING: HIR 701 has a net charge of 0.5140 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 0.6596379 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): -17.70000 30.51900 ymin,ymax (A): 3.512000 48.23600 zmin,zma (A): -16.87700 37.09200 x,y,z range (A): 48.21900 44.72400 53.96900 scale (grids/A): 0.6596379 object centre (A): 6.409500 25.87400 10.10750 number of atom coordinates read : 2300 total number of charged atoms : 2231 net assigned charge : 4.420008 assigned positive charge : 344.7751 centred at (gu) : 89.32885 91.67360 89.84711 assigned negative charge : -340.3558 centred at (gu) : 89.28394 91.59218 89.92834 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6788 nv = 96 ne = 84 npr = 46096 no. pairs analyzed = 46096 no. exposed pairs = 2942 no. arc points = 20169 no. surface atoms = 1010 nbur = 1290 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 3729 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.2600000 number of dielectric boundary points 3400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1967 ## 171 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8044 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5474783E-08 -3.0478378E-09 midg,1,midg; midg,igrid,midg -2.0967805E-09 3.5078816E-08 1,midg,midg; igrid,midg,midg 3.5207697E-09 1.6159794E-08 gauss-seidel spectral radius is 0.9880630 estimated iterations to convergence 75 setup time was (sec) 0.5400000 now iterating at: 15:47:06 rms-change max change #iterations 0.1580426 28.50430 at 10iterations 1.6672075E-02 2.462608 at 20iterations 1.8176720E-03 0.2457695 at 30iterations 2.1919890E-04 3.6334991E-02 at 40iterations 3.8103295E-05 5.1345825E-03 at 50iterations finished qdiffx linear iterations at : 15:47:09 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 3.8103295E-05 5.1345825E-03 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 15:47:10 4.241u 0.295s 0:04.83 93.7% 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 8 2011 at 15:47:10 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2300 !!! WARNING: HIR 701 has a net charge of 0.5140 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 1.978914 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): -17.70000 30.51900 ymin,ymax (A): 3.512000 48.23600 zmin,zma (A): -16.87700 37.09200 x,y,z range (A): 48.21900 44.72400 53.96900 scale (grids/A): 1.978914 object centre (A): 6.409500 25.87400 10.10750 number of atom coordinates read : 2300 total number of charged atoms : 2231 net assigned charge : 4.420008 assigned positive charge : 344.7751 centred at (gu) : 87.98647 95.02029 89.54081 assigned negative charge : -340.3558 centred at (gu) : 87.85162 94.77670 89.78494 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20169 grid for indexing accessible points = 1.400000 m= 26960 mr = 51068 m= 4598 mr = 19809 m= 299 mr = 2936 m= 10 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 166 time to turn everything in is 0.5600000 number of dielectric boundary points 31225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 117 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 17616 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) : 0.6596379 object centre at (A) : 6.409500 25.87400 10.10750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5759609E-02 -7.1107913E-03 midg,1,midg; midg,igrid,midg -2.8569254E-03 3.1781666E-02 1,midg,midg; igrid,midg,midg -3.6592539E-02 2.1101683E-02 gauss-seidel spectral radius is 0.9987031 estimated iterations to convergence 220 setup time was (sec) 0.8800000 now iterating at: 15:47:11 rms-change max change #iterations 4.262246 182.6245 at 10iterations 2.036902 76.40866 at 20iterations 0.9720107 32.59386 at 30iterations 0.4628902 15.02887 at 40iterations 0.2215987 7.054344 at 50iterations 0.1062686 3.133969 at 60iterations 5.0707575E-02 1.511860 at 70iterations 2.4241941E-02 0.7437010 at 80iterations 1.1539086E-02 0.3469181 at 90iterations 5.5474327E-03 0.1787224 at 100iterations 2.6483375E-03 8.5433960E-02 at 110iterations 1.2736025E-03 3.9169312E-02 at 120iterations finished qdiffx linear iterations at : 15:47:20 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 1.2736025E-03 3.9169312E-02 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.560000 DelPhi exited at 15:47:20 9.558u 0.260s 0:10.08 97.3% 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 Sat Oct 8 2011 at 15:47:20 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2300 !!! WARNING: HIR 701 has a net charge of 0.5140 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 2.968371 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): -17.70000 30.51900 ymin,ymax (A): 3.512000 48.23600 zmin,zma (A): -16.87700 37.09200 x,y,z range (A): 48.21900 44.72400 53.96900 scale (grids/A): 2.968371 object centre (A): 6.409500 25.87400 10.10750 number of atom coordinates read : 2300 total number of charged atoms : 2231 net assigned charge : 4.420008 assigned positive charge : 344.7751 centred at (gu) : 86.97952 97.53028 89.31104 assigned negative charge : -340.3558 centred at (gu) : 86.77743 97.16491 89.67735 start vw surface at 0.1200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 169573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20169 grid for indexing accessible points = 1.400000 m= 86302 mr = 123702 m= 32438 mr = 70508 m= 8574 mr = 26119 m= 1388 mr = 6552 m= 100 mr = 924 m= 1 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 588 time to turn everything in is 1.460000 number of dielectric boundary points 70522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.620000 number of grid points assigned charge 17848 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) : 1.978914 object centre at (A) : 6.409500 25.87400 10.10750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2517653 -0.1699920 midg,1,midg; midg,igrid,midg -5.4265663E-02 0.2693265 1,midg,midg; igrid,midg,midg -0.5479829 0.2134415 gauss-seidel spectral radius is 0.9992778 estimated iterations to convergence 294 setup time was (sec) 1.810000 now iterating at: 15:47:22 rms-change max change #iterations 9.940578 426.6293 at 10iterations 5.847118 130.9270 at 20iterations 3.437003 76.69411 at 30iterations 2.018004 38.97422 at 40iterations 1.179479 21.82951 at 50iterations 0.6903791 12.69159 at 60iterations 0.4016612 7.201452 at 70iterations 0.2334642 4.557387 at 80iterations 0.1357394 2.861242 at 90iterations 7.8899994E-02 1.724890 at 100iterations 4.5784771E-02 0.7891111 at 110iterations 2.6549574E-02 0.4754486 at 120iterations 1.5380656E-02 0.2754960 at 130iterations 8.9320885E-03 0.1605759 at 140iterations 5.1819081E-03 9.8256588E-02 at 150iterations 3.0102860E-03 5.7660341E-02 at 160iterations 1.7466340E-03 3.3515692E-02 at 170iterations 1.0160652E-03 1.8592834E-02 at 180iterations finished qdiffx linear iterations at : 15:47:35 total time elapsed so far: 15.08000 # loops : 180 mean,max change (kT/e) : 1.0160652E-03 1.8592834E-02 energy calculations done at 15.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.26000 DelPhi exited at 15:47:36 15.262u 0.283s 0:15.82 98.2% 0+0k 0+0io 0pf+0w