Sat Oct 15 13:42:12 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+sph.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 = amb.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 15 2011 at 13:42:12 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2820 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: 0.6325065 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): 3.130000 57.42100 ymin,ymax (A): -4.108000 52.17600 zmin,zma (A): -31.41800 23.34900 x,y,z range (A): 54.29100 56.28400 54.76700 scale (grids/A): 0.6325065 object centre (A): 30.27550 24.03400 -4.034500 number of atom coordinates read : 2820 total number of charged atoms : 2664 net assigned charge : -5.499990 assigned positive charge : 423.3112 centred at (gu) : 90.69594 87.44160 89.85862 assigned negative charge : -428.8122 centred at (gu) : 90.65434 87.30789 89.66296 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7642 nv = 96 ne = 84 npr = 56574 no. pairs analyzed = 56574 no. exposed pairs = 3614 no. arc points = 25757 no. surface atoms = 1207 nbur = 1613 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 394 mr = 4056 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 95 time to turn everything in is 0.3200000 number of dielectric boundary points 3942 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2633 ## 257 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9296 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7574174E-08 1.3501222E-08 midg,1,midg; midg,igrid,midg -3.5261206E-08 4.3296944E-09 1,midg,midg; igrid,midg,midg -8.8877963E-09 -1.8722144E-09 gauss-seidel spectral radius is 0.9870778 estimated iterations to convergence 72 setup time was (sec) 0.5800000 now iterating at: 13:42:13 rms-change max change #iterations 0.1403031 20.77707 at 10iterations 1.3841239E-02 1.848898 at 20iterations 1.3604278E-03 0.1846676 at 30iterations 1.3808590E-04 2.2558212E-02 at 40iterations 1.6696269E-05 2.8457642E-03 at 50iterations finished qdiffx linear iterations at : 13:42:17 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 1.6696269E-05 2.8457642E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 13:42:17 4.141u 0.414s 0:04.97 91.5% 0+0k 0+0io 6pf+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 15 2011 at 13:42:17 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2820 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: 1.897520 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): 3.130000 57.42100 ymin,ymax (A): -4.108000 52.17600 zmin,zma (A): -31.41800 23.34900 x,y,z range (A): 54.29100 56.28400 54.76700 scale (grids/A): 1.897520 object centre (A): 30.27550 24.03400 -4.034500 number of atom coordinates read : 2820 total number of charged atoms : 2664 net assigned charge : -5.499990 assigned positive charge : 423.3112 centred at (gu) : 92.08699 82.32391 89.57504 assigned negative charge : -428.8122 centred at (gu) : 91.96275 81.92336 88.98867 start vw surface at 0.1100000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 82265 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25757 grid for indexing accessible points = 1.400000 m= 27976 mr = 55952 m= 4346 mr = 19843 m= 266 mr = 2637 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 3583 time to turn everything in is 0.6200000 number of dielectric boundary points 36342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 193 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 20966 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) : 0.6325065 object centre at (A) : 30.27550 24.03400 -4.034500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4239701E-02 -4.3281242E-03 midg,1,midg; midg,igrid,midg -5.5911090E-02 2.2340953E-02 1,midg,midg; igrid,midg,midg -4.1252326E-02 -1.4170852E-02 gauss-seidel spectral radius is 0.9986483 estimated iterations to convergence 216 setup time was (sec) 0.9300000 now iterating at: 13:42:19 rms-change max change #iterations 4.432835 186.1199 at 10iterations 2.077397 69.69136 at 20iterations 0.9794017 29.34961 at 30iterations 0.4578885 13.94628 at 40iterations 0.2156536 6.632505 at 50iterations 0.1011503 3.209764 at 60iterations 4.7495816E-02 1.441721 at 70iterations 2.2327021E-02 0.7109039 at 80iterations 1.0474258E-02 0.3599854 at 90iterations 4.9396008E-03 0.1422095 at 100iterations 2.3361975E-03 7.2914124E-02 at 110iterations 1.1026101E-03 3.1972885E-02 at 120iterations finished qdiffx linear iterations at : 13:42:28 total time elapsed so far: 10.10000 # loops : 120 mean,max change (kT/e) : 1.1026101E-03 3.1972885E-02 energy calculations done at 10.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.28000 DelPhi exited at 13:42:29 10.288u 0.501s 0:11.18 96.4% 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 15 2011 at 13:42:29 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2820 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: 2.846279 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): 3.130000 57.42100 ymin,ymax (A): -4.108000 52.17600 zmin,zma (A): -31.41800 23.34900 x,y,z range (A): 54.29100 56.28400 54.76700 scale (grids/A): 2.846279 object centre (A): 30.27550 24.03400 -4.034500 number of atom coordinates read : 2820 total number of charged atoms : 2664 net assigned charge : -5.499990 assigned positive charge : 423.3112 centred at (gu) : 93.13020 78.48559 89.36231 assigned negative charge : -428.8122 centred at (gu) : 92.94398 77.88490 88.48279 start vw surface at 0.1200000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 190500 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25757 grid for indexing accessible points = 1.400000 m= 91777 mr = 135958 m= 31552 mr = 73765 m= 7767 mr = 24540 m= 1185 mr = 5733 m= 67 mr = 795 m= 0 mr = 25 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 12493 time to turn everything in is 1.670000 number of dielectric boundary points 82032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 21311 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) : 1.897520 object centre at (A) : 30.27550 24.03400 -4.034500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6882375 -5.0998203E-02 midg,1,midg; midg,igrid,midg -0.6058246 0.2315074 1,midg,midg; igrid,midg,midg -0.4169953 -0.4006779 gauss-seidel spectral radius is 0.9992736 estimated iterations to convergence 293 setup time was (sec) 1.990000 now iterating at: 13:42:31 rms-change max change #iterations 10.58652 432.1595 at 10iterations 6.226482 130.0984 at 20iterations 3.643850 79.61764 at 30iterations 2.121847 44.79890 at 40iterations 1.232596 26.96978 at 50iterations 0.7160980 13.65766 at 60iterations 0.4144985 7.814873 at 70iterations 0.2398819 4.744769 at 80iterations 0.1388893 2.522079 at 90iterations 8.0269940E-02 1.912150 at 100iterations 4.6338640E-02 0.7782249 at 110iterations 2.6836555E-02 0.4836540 at 120iterations 1.5467693E-02 0.2902703 at 130iterations 8.9628231E-03 0.1518168 at 140iterations 5.1827626E-03 9.6340179E-02 at 150iterations 2.9898218E-03 5.2484512E-02 at 160iterations 1.7397732E-03 3.3618450E-02 at 170iterations 1.0105881E-03 2.0004272E-02 at 180iterations finished qdiffx linear iterations at : 13:42:46 total time elapsed so far: 17.10000 # loops : 180 mean,max change (kT/e) : 1.0105881E-03 2.0004272E-02 energy calculations done at 17.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.27000 DelPhi exited at 13:42:47 17.277u 0.536s 0:18.18 97.9% 0+0k 0+0io 0pf+0w