Tue Nov 22 14:19:56 PST 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 Nov 22 2011 at 14:20:01 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6068561 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): -24.05200 34.61100 ymin,ymax (A): -19.04800 20.62900 zmin,zma (A): -3.236000 39.05000 x,y,z range (A): 58.66300 39.67700 42.28600 scale (grids/A): 0.6068561 object centre (A): 5.279500 0.7904997 17.90700 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 5.000011 assigned positive charge : 287.5280 centred at (gu) : 89.91335 90.20912 90.20810 assigned negative charge : -282.5283 centred at (gu) : 89.91975 90.28091 90.32943 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4820 nv = 96 ne = 84 npr = 39598 no. pairs analyzed = 39598 no. exposed pairs = 2546 no. arc points = 18082 no. surface atoms = 869 nbur = 1065 mkacc time = 9.0000004E-02 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= 216 mr = 2491 m= 3 mr = 15 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 0.2400000 number of dielectric boundary points 2533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1843 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 5875 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3138206E-09 -1.4163916E-09 midg,1,midg; midg,igrid,midg 4.7974438E-09 3.2562758E-10 1,midg,midg; igrid,midg,midg 2.9559228E-09 2.4347322E-09 gauss-seidel spectral radius is 0.9858894 estimated iterations to convergence 69 setup time was (sec) 0.4800000 now iterating at: 14:20:04 rms-change max change #iterations 0.1015009 22.94979 at 10iterations 8.9500910E-03 1.441825 at 20iterations 7.6738436E-04 0.1474571 at 30iterations 6.4681451E-05 1.3160706E-02 at 40iterations 5.5976802E-06 8.6593628E-04 at 50iterations finished qdiffx linear iterations at : 14:20:13 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 5.5976802E-06 8.6593628E-04 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 14:20:14 3.386u 0.155s 0:13.79 25.5% 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 Nov 22 2011 at 14:20:16 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.820568 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): -24.05200 34.61100 ymin,ymax (A): -19.04800 20.62900 zmin,zma (A): -3.236000 39.05000 x,y,z range (A): 58.66300 39.67700 42.28600 scale (grids/A): 1.820568 object centre (A): 5.279500 0.7904997 17.90700 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 5.000011 assigned positive charge : 287.5280 centred at (gu) : 89.74002 90.62746 90.62439 assigned negative charge : -282.5283 centred at (gu) : 89.75935 90.84302 90.98863 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 52106 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18082 grid for indexing accessible points = 1.400000 m= 17980 mr = 34763 m= 2301 mr = 12993 m= 83 mr = 1206 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 23496 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 14090 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) : 0.6068561 object centre at (A) : 5.279500 0.7904997 17.90700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.6362893E-03 -2.8154612E-04 midg,1,midg; midg,igrid,midg 6.3029337E-03 2.4515009E-03 1,midg,midg; igrid,midg,midg 4.3790214E-02 3.3091903E-02 gauss-seidel spectral radius is 0.9984328 estimated iterations to convergence 200 setup time was (sec) 0.6900000 now iterating at: 14:20:20 rms-change max change #iterations 3.299571 180.6017 at 10iterations 1.452824 54.46858 at 20iterations 0.6467083 25.56764 at 30iterations 0.2851206 10.49094 at 40iterations 0.1263122 5.349207 at 50iterations 5.5845212E-02 2.169798 at 60iterations 2.4898916E-02 0.8945007 at 70iterations 1.1014996E-02 0.4518018 at 80iterations 4.8603560E-03 0.1864042 at 90iterations 2.1540232E-03 7.6552391E-02 at 100iterations 9.5462130E-04 4.5333862E-02 at 110iterations 4.2460728E-04 1.6989946E-02 at 120iterations finished qdiffx linear iterations at : 14:20:45 total time elapsed so far: 7.130000 # loops : 120 mean,max change (kT/e) : 4.2460728E-04 1.6989946E-02 energy calculations done at 7.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.310000 DelPhi exited at 14:20:46 7.316u 0.182s 0:31.66 23.6% 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 Nov 22 2011 at 14:20:48 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: 243 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.730852 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): -24.05200 34.61100 ymin,ymax (A): -19.04800 20.62900 zmin,zma (A): -3.236000 39.05000 x,y,z range (A): 58.66300 39.67700 42.28600 scale (grids/A): 2.730852 object centre (A): 5.279500 0.7904997 17.90700 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 5.000011 assigned positive charge : 287.5280 centred at (gu) : 89.61011 90.94105 90.93659 assigned negative charge : -282.5283 centred at (gu) : 89.63914 91.26450 91.48299 start vw surface at 0.1400000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 120279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18082 grid for indexing accessible points = 1.400000 m= 59048 mr = 84490 m= 19642 mr = 47605 m= 3722 mr = 15510 m= 309 mr = 2467 m= 10 mr = 171 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9900000 number of dielectric boundary points 52767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 14416 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) : 1.820568 object centre at (A) : 5.279500 0.7904997 17.90700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7511842E-02 3.2168426E-02 midg,1,midg; midg,igrid,midg 4.7308400E-02 5.4259468E-02 1,midg,midg; igrid,midg,midg 0.6118934 0.3575656 gauss-seidel spectral radius is 0.9991888 estimated iterations to convergence 277 setup time was (sec) 1.280000 now iterating at: 14:20:55 rms-change max change #iterations 7.944149 317.4961 at 10iterations 4.554044 119.4958 at 20iterations 2.586429 71.01765 at 30iterations 1.460595 35.90291 at 40iterations 0.8246748 19.40312 at 50iterations 0.4638970 10.79645 at 60iterations 0.2602887 5.591511 at 70iterations 0.1456447 3.151620 at 80iterations 8.1854276E-02 2.040329 at 90iterations 4.5849510E-02 1.124144 at 100iterations 2.5595130E-02 0.6013455 at 110iterations 1.4374541E-02 0.3257141 at 120iterations 8.0220252E-03 0.1871815 at 130iterations 4.4995691E-03 0.1159668 at 140iterations 2.5151733E-03 5.6789398E-02 at 150iterations 1.4052076E-03 3.1219482E-02 at 160iterations 7.8527769E-04 1.7600060E-02 at 170iterations 4.3890387E-04 9.5005035E-03 at 180iterations finished qdiffx linear iterations at : 14:21:26 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 4.3890387E-04 9.5005035E-03 energy calculations done at 11.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.80000 DelPhi exited at 14:21:28 11.802u 0.160s 0:40.30 29.6% 0+0k 0+0io 0pf+0w