Sun Oct 9 08:51:24 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 Sun Oct 9 2011 at 08:51:24 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6032 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4567265 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): 4.662000 82.60800 ymin,ymax (A): -22.97600 44.00400 zmin,zma (A): -6.238000 57.36100 x,y,z range (A): 77.94600 66.98000 63.59900 scale (grids/A): 0.4567265 object centre (A): 43.63500 10.51400 25.56150 number of atom coordinates read : 6032 total number of charged atoms : 5862 net assigned charge : -2.985992 assigned positive charge : 910.2100 centred at (gu) : 89.32190 90.49434 90.52254 assigned negative charge : -913.2038 centred at (gu) : 89.21434 90.52008 90.55870 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7634 nv = 96 ne = 84 npr = 120911 no. pairs analyzed = 120911 no. exposed pairs = 7586 no. arc points = 52619 no. surface atoms = 2537 nbur = 3495 mkacc time = 0.2100000 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 = 1.876000 m= 247 mr = 3774 m= 0 mr = 4 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3900000 number of dielectric boundary points 4103 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4713 ## 915 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 10511 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5501281E-12 -1.3738019E-11 midg,1,midg; midg,igrid,midg 3.3428800E-12 -1.0545513E-11 1,midg,midg; igrid,midg,midg -3.6936870E-11 1.9752998E-11 gauss-seidel spectral radius is 0.9756100 estimated iterations to convergence 53 setup time was (sec) 0.5800000 now iterating at: 08:51:25 rms-change max change #iterations 4.2856779E-02 6.399384 at 10iterations 2.0325808E-03 0.4220695 at 20iterations 2.7209456E-04 7.2261810E-02 at 30iterations 6.7816203E-05 1.6288757E-02 at 40iterations 1.9467512E-05 4.0740967E-03 at 50iterations finished qdiffx linear iterations at : 08:51:29 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 1.9467512E-05 4.0740967E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 08:51:30 3.703u 0.388s 0:05.74 71.0% 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 Sun Oct 9 2011 at 08:51:30 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6032 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.370179 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): 4.662000 82.60800 ymin,ymax (A): -22.97600 44.00400 zmin,zma (A): -6.238000 57.36100 x,y,z range (A): 77.94600 66.98000 63.59900 scale (grids/A): 1.370179 object centre (A): 43.63500 10.51400 25.56150 number of atom coordinates read : 6032 total number of charged atoms : 5862 net assigned charge : -2.985992 assigned positive charge : 910.2100 centred at (gu) : 87.96419 91.48109 91.56609 assigned negative charge : -913.2038 centred at (gu) : 87.64277 91.55990 91.67586 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 88765 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52619 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.764000 m= 22099 mr = 59803 m= 1317 mr = 13589 m= 14 mr = 412 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 970 time to turn everything in is 0.4500000 number of dielectric boundary points 38391 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 994 ## 28 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 41970 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) : 0.4567265 object centre at (A) : 43.63500 10.51400 25.56150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9572204E-04 -1.9336973E-03 midg,1,midg; midg,igrid,midg -1.0943464E-03 -3.8833187E-03 1,midg,midg; igrid,midg,midg -6.0122912E-03 5.4159011E-03 gauss-seidel spectral radius is 0.9976946 estimated iterations to convergence 166 setup time was (sec) 0.6600000 now iterating at: 08:51:31 rms-change max change #iterations 3.322470 148.7434 at 10iterations 1.239963 42.99892 at 20iterations 0.4629048 14.86556 at 30iterations 0.1735124 5.503862 at 40iterations 6.5142952E-02 2.339150 at 50iterations 2.4352621E-02 0.7680540 at 60iterations 9.1688130E-03 0.3011646 at 70iterations 3.4549781E-03 0.1431007 at 80iterations 1.3219952E-03 4.7365189E-02 at 90iterations 5.1798683E-04 2.0427704E-02 at 100iterations 2.1672281E-04 8.9302063E-03 at 110iterations 1.0157497E-04 4.6501160E-03 at 120iterations finished qdiffx linear iterations at : 08:51:41 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 1.0157497E-04 4.6501160E-03 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 08:51:42 8.001u 0.695s 0:12.26 70.8% 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 Sun Oct 9 2011 at 08:51:42 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6032 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.055269 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): 4.662000 82.60800 ymin,ymax (A): -22.97600 44.00400 zmin,zma (A): -6.238000 57.36100 x,y,z range (A): 77.94600 66.98000 63.59900 scale (grids/A): 2.055269 object centre (A): 43.63500 10.51400 25.56150 number of atom coordinates read : 6032 total number of charged atoms : 5862 net assigned charge : -2.985992 assigned positive charge : 910.2100 centred at (gu) : 86.94587 92.22108 92.34856 assigned negative charge : -913.2038 centred at (gu) : 86.46396 92.33969 92.51351 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 207959 reading accessible surface arcs data from file ARCDAT no. of arc points read = 52619 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 84414 mr = 148486 m= 16747 mr = 63481 m= 1550 mr = 11251 m= 40 mr = 730 m= 0 mr = 6 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 3314 time to turn everything in is 1.060000 number of dielectric boundary points 86756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 46504 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) : 1.370179 object centre at (A) : 43.63500 10.51400 25.56150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8524260E-03 -5.4692917E-02 midg,1,midg; midg,igrid,midg 5.2672043E-03 -8.5686967E-02 1,midg,midg; igrid,midg,midg -3.1122478E-02 -7.4922763E-02 gauss-seidel spectral radius is 0.9990683 estimated iterations to convergence 259 setup time was (sec) 1.300000 now iterating at: 08:51:44 rms-change max change #iterations 9.771708 272.1904 at 10iterations 5.485785 127.5791 at 20iterations 3.039511 71.13182 at 30iterations 1.679828 44.80878 at 40iterations 0.9253227 22.86424 at 50iterations 0.5064381 11.61629 at 60iterations 0.2764333 5.898677 at 70iterations 0.1508119 3.063747 at 80iterations 8.1976011E-02 1.684551 at 90iterations 4.4538256E-02 1.012031 at 100iterations 2.4159594E-02 0.5279160 at 110iterations 1.3104197E-02 0.2662609 at 120iterations 7.1038641E-03 0.1500235 at 130iterations 3.8358399E-03 8.0688477E-02 at 140iterations 2.0872948E-03 3.8665771E-02 at 150iterations 1.1304471E-03 2.1910191E-02 at 160iterations 6.1650045E-04 1.3917923E-02 at 170iterations 3.3847190E-04 6.0958862E-03 at 180iterations finished qdiffx linear iterations at : 08:51:55 total time elapsed so far: 12.80000 # loops : 180 mean,max change (kT/e) : 3.3847190E-04 6.0958862E-03 energy calculations done at 12.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 08:51:56 12.934u 0.237s 0:13.59 96.8% 0+0k 0+0io 0pf+0w