Sat Oct 8 19:49:49 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 19:49:49 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2410 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 522 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6602007 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): -30.72800 17.71400 ymin,ymax (A): -24.24500 23.20000 zmin,zma (A): -12.09600 41.82700 x,y,z range (A): 48.44200 47.44500 53.92300 scale (grids/A): 0.6602007 object centre (A): -6.507000 -0.5225000 14.86550 number of atom coordinates read : 2410 total number of charged atoms : 2271 net assigned charge : 2.500008 assigned positive charge : 362.1264 centred at (gu) : 88.75761 89.29590 89.67931 assigned negative charge : -359.6268 centred at (gu) : 88.63670 89.35464 89.62947 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6899 nv = 96 ne = 84 npr = 51142 no. pairs analyzed = 51142 no. exposed pairs = 2767 no. arc points = 19870 no. surface atoms = 921 nbur = 1489 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3982 m= 0 mr = 59 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 218 time to turn everything in is 0.3500000 number of dielectric boundary points 3261 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1858 ## 165 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8218 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7650127E-09 1.4759054E-08 midg,1,midg; midg,igrid,midg 2.0147205E-08 -3.5853918E-09 1,midg,midg; igrid,midg,midg -2.0828596E-08 2.2092275E-08 gauss-seidel spectral radius is 0.9880873 estimated iterations to convergence 75 setup time was (sec) 0.6100000 now iterating at: 19:49:50 rms-change max change #iterations 0.1617083 22.30160 at 10iterations 1.7262205E-02 2.290275 at 20iterations 1.8378425E-03 0.2910709 at 30iterations 1.9902911E-04 2.7366638E-02 at 40iterations 2.1045251E-05 2.6402473E-03 at 50iterations finished qdiffx linear iterations at : 19:49:53 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 2.1045251E-05 2.6402473E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 19:49:54 4.055u 0.261s 0:04.60 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 8 2011 at 19:49:54 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2410 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 522 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.980602 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): -30.72800 17.71400 ymin,ymax (A): -24.24500 23.20000 zmin,zma (A): -12.09600 41.82700 x,y,z range (A): 48.44200 47.44500 53.92300 scale (grids/A): 1.980602 object centre (A): -6.507000 -0.5225000 14.86550 number of atom coordinates read : 2410 total number of charged atoms : 2271 net assigned charge : 2.500008 assigned positive charge : 362.1264 centred at (gu) : 86.27229 87.88754 89.03756 assigned negative charge : -359.6268 centred at (gu) : 85.90996 88.06372 88.88847 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 74310 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19870 grid for indexing accessible points = 1.400000 m= 27569 mr = 52492 m= 4834 mr = 20808 m= 361 mr = 3314 m= 3 mr = 157 m= 0 mr = 2 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 5427 time to turn everything in is 0.6800000 number of dielectric boundary points 30304 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 17952 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) : 0.6602007 object centre at (A) : -6.507000 -0.5225000 14.86550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3043474E-02 -1.1142395E-02 midg,1,midg; midg,igrid,midg 1.6826510E-02 8.1745181E-03 1,midg,midg; igrid,midg,midg 8.9677703E-03 5.7249043E-02 gauss-seidel spectral radius is 0.9987091 estimated iterations to convergence 220 setup time was (sec) 0.9700000 now iterating at: 19:49:55 rms-change max change #iterations 4.363120 182.9505 at 10iterations 2.086750 65.67683 at 20iterations 0.9973282 32.13206 at 30iterations 0.4784080 14.95939 at 40iterations 0.2289468 7.992111 at 50iterations 0.1094025 3.413582 at 60iterations 5.2519299E-02 1.745033 at 70iterations 2.5107475E-02 0.7626648 at 80iterations 1.2007275E-02 0.3978519 at 90iterations 5.7336846E-03 0.1990433 at 100iterations 2.7476228E-03 8.9996338E-02 at 110iterations 1.3176224E-03 4.2690277E-02 at 120iterations finished qdiffx linear iterations at : 19:50:03 total time elapsed so far: 9.230000 # loops : 120 mean,max change (kT/e) : 1.3176224E-03 4.2690277E-02 energy calculations done at 9.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.410000 DelPhi exited at 19:50:04 9.413u 0.270s 0:09.95 97.2% 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 19:50:04 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: 289 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2410 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN5 522 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.970903 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): -30.72800 17.71400 ymin,ymax (A): -24.24500 23.20000 zmin,zma (A): -12.09600 41.82700 x,y,z range (A): 48.44200 47.44500 53.92300 scale (grids/A): 2.970903 object centre (A): -6.507000 -0.5225000 14.86550 number of atom coordinates read : 2410 total number of charged atoms : 2271 net assigned charge : 2.500008 assigned positive charge : 362.1264 centred at (gu) : 84.40842 86.83125 88.55614 assigned negative charge : -359.6268 centred at (gu) : 83.86493 87.09565 88.33277 start vw surface at 0.1500000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 171848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19870 grid for indexing accessible points = 1.400000 m= 88402 mr = 126800 m= 33280 mr = 73549 m= 9015 mr = 27370 m= 1508 mr = 7036 m= 118 mr = 1094 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 18811 time to turn everything in is 1.720000 number of dielectric boundary points 68262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 18168 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) : 1.980602 object centre at (A) : -6.507000 -0.5225000 14.86550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1071688 -0.1383827 midg,1,midg; midg,igrid,midg 0.1825666 8.3134152E-02 1,midg,midg; igrid,midg,midg 0.1537713 0.6436684 gauss-seidel spectral radius is 0.9992672 estimated iterations to convergence 292 setup time was (sec) 2.040000 now iterating at: 19:50:06 rms-change max change #iterations 9.967509 469.9005 at 10iterations 5.750305 155.6613 at 20iterations 3.324080 64.22282 at 30iterations 1.921634 36.89441 at 40iterations 1.108247 21.89921 at 50iterations 0.6395993 12.65844 at 60iterations 0.3688988 6.763424 at 70iterations 0.2125458 3.793225 at 80iterations 0.1223099 2.282446 at 90iterations 7.0623182E-02 1.263428 at 100iterations 4.0633131E-02 0.7415199 at 110iterations 2.3422880E-02 0.4319553 at 120iterations 1.3502932E-02 0.2291870 at 130iterations 7.7715749E-03 0.1338501 at 140iterations 4.4778734E-03 8.4927738E-02 at 150iterations 2.5918153E-03 4.7153473E-02 at 160iterations 1.4981385E-03 2.9176712E-02 at 170iterations 8.6653687E-04 1.6738892E-02 at 180iterations finished qdiffx linear iterations at : 19:50:19 total time elapsed so far: 15.57000 # loops : 180 mean,max change (kT/e) : 8.6653687E-04 1.6738892E-02 energy calculations done at 15.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.76000 DelPhi exited at 19:50:20 15.757u 0.295s 0:16.36 98.0% 0+0k 0+0io 0pf+0w