Mon Oct 10 20:16:35 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 Mon Oct 10 2011 at 20:16:35 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5964249 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): -10.78000 40.93600 ymin,ymax (A): 29.97300 89.66199 zmin,zma (A): -13.02400 44.50600 x,y,z range (A): 51.71600 59.68900 57.52999 scale (grids/A): 0.5964249 object centre (A): 15.07800 59.81750 15.74100 number of atom coordinates read : 2777 total number of charged atoms : 2639 net assigned charge : 1.000026 assigned positive charge : 417.1935 centred at (gu) : 90.10022 89.15369 90.46823 assigned negative charge : -416.1946 centred at (gu) : 90.13873 89.18113 90.52856 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6563 nv = 96 ne = 84 npr = 55270 no. pairs analyzed = 55270 no. exposed pairs = 3897 no. arc points = 27701 no. surface atoms = 1289 nbur = 1488 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3183 m= 0 mr = 17 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2788 ## 281 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8256 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2278746E-09 -1.9440318E-09 midg,1,midg; midg,igrid,midg 1.6309939E-09 -4.7209903E-10 1,midg,midg; igrid,midg,midg 1.6874457E-09 -9.9196285E-10 gauss-seidel spectral radius is 0.9854773 estimated iterations to convergence 68 setup time was (sec) 0.5900000 now iterating at: 20:16:36 rms-change max change #iterations 0.1081906 19.27011 at 10iterations 9.2473244E-03 1.381644 at 20iterations 9.0963248E-04 0.1530933 at 30iterations 1.3830270E-04 2.3603439E-02 at 40iterations 3.0133862E-05 4.9457550E-03 at 50iterations finished qdiffx linear iterations at : 20:16:39 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 3.0133862E-05 4.9457550E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 20:16:40 3.581u 0.201s 0:04.60 82.1% 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 Mon Oct 10 2011 at 20:16:40 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 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: 1.789275 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): -10.78000 40.93600 ymin,ymax (A): 29.97300 89.66199 zmin,zma (A): -13.02400 44.50600 x,y,z range (A): 51.71600 59.68900 57.52999 scale (grids/A): 1.789275 object centre (A): 15.07800 59.81750 15.74100 number of atom coordinates read : 2777 total number of charged atoms : 2639 net assigned charge : 1.000026 assigned positive charge : 417.1935 centred at (gu) : 90.30007 87.46079 91.40414 assigned negative charge : -416.1946 centred at (gu) : 90.41595 87.54303 91.58558 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 69917 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27701 grid for indexing accessible points = 1.400000 m= 23898 mr = 44828 m= 3452 mr = 16394 m= 117 mr = 1873 m= 0 mr = 12 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 149 time to turn everything in is 0.5900000 number of dielectric boundary points 34277 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 220 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20581 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) : 0.5964249 object centre at (A) : 15.07800 59.81750 15.74100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4807628E-04 -3.1357281E-02 midg,1,midg; midg,igrid,midg 1.4557009E-02 -7.6667201E-03 1,midg,midg; igrid,midg,midg 1.4222858E-02 -1.6304669E-03 gauss-seidel spectral radius is 0.9984943 estimated iterations to convergence 204 setup time was (sec) 0.9200000 now iterating at: 20:16:41 rms-change max change #iterations 3.938035 198.2469 at 10iterations 1.761209 64.72594 at 20iterations 0.7892917 28.28045 at 30iterations 0.3561606 12.62286 at 40iterations 0.1599833 5.337596 at 50iterations 7.1928769E-02 2.275915 at 60iterations 3.2431182E-02 1.196621 at 70iterations 1.4637209E-02 0.4793987 at 80iterations 6.6495305E-03 0.2621918 at 90iterations 3.0100432E-03 0.1012003 at 100iterations 1.3769733E-03 4.5897484E-02 at 110iterations 6.4147357E-04 2.1956444E-02 at 120iterations finished qdiffx linear iterations at : 20:16:48 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 6.4147357E-04 2.1956444E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.110000 DelPhi exited at 20:16:49 8.112u 0.187s 0:08.81 94.0% 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 Mon Oct 10 2011 at 20:16:50 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 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: 2.683912 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): -10.78000 40.93600 ymin,ymax (A): 29.97300 89.66199 zmin,zma (A): -13.02400 44.50600 x,y,z range (A): 51.71600 59.68900 57.52999 scale (grids/A): 2.683912 object centre (A): 15.07800 59.81750 15.74100 number of atom coordinates read : 2777 total number of charged atoms : 2639 net assigned charge : 1.000026 assigned positive charge : 417.1935 centred at (gu) : 90.44998 86.19113 92.10590 assigned negative charge : -416.1946 centred at (gu) : 90.62395 86.31454 92.37831 start vw surface at 0.1800000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 161874 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27701 grid for indexing accessible points = 1.400000 m= 76780 mr = 110326 m= 27174 mr = 59492 m= 5823 mr = 20790 m= 488 mr = 3995 m= 10 mr = 213 m= 0 mr = 0 time to grow re-entrant surface = 0.7500001 no. cavity mid-points inaccessible to solvent = 475 time to turn everything in is 1.340000 number of dielectric boundary points 77333 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 21106 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) : 1.789275 object centre at (A) : 15.07800 59.81750 15.74100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3935113E-02 -0.4702907 midg,1,midg; midg,igrid,midg 0.3227789 -2.8766781E-02 1,midg,midg; igrid,midg,midg 0.1469985 -5.4377154E-02 gauss-seidel spectral radius is 0.9992337 estimated iterations to convergence 285 setup time was (sec) 1.650000 now iterating at: 20:16:52 rms-change max change #iterations 9.689437 403.3166 at 10iterations 5.663307 140.3149 at 20iterations 3.272169 76.94823 at 30iterations 1.886046 39.00453 at 40iterations 1.086275 22.35096 at 50iterations 0.6206698 13.84259 at 60iterations 0.3553652 6.977276 at 70iterations 0.2036754 3.761459 at 80iterations 0.1160177 2.600571 at 90iterations 6.6294372E-02 1.305117 at 100iterations 3.7817415E-02 0.7398472 at 110iterations 2.1568678E-02 0.4307556 at 120iterations 1.2329173E-02 0.2341042 at 130iterations 7.0348280E-03 0.1305523 at 140iterations 4.0294454E-03 7.7001572E-02 at 150iterations 2.3204652E-03 5.3529739E-02 at 160iterations 1.3516758E-03 2.9485703E-02 at 170iterations 7.9606561E-04 1.7135620E-02 at 180iterations finished qdiffx linear iterations at : 20:17:02 total time elapsed so far: 11.93000 # loops : 180 mean,max change (kT/e) : 7.9606561E-04 1.7135620E-02 energy calculations done at 11.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.13000 DelPhi exited at 20:17:02 12.132u 0.160s 0:12.67 97.0% 0+0k 0+0io 0pf+0w