Mon Oct 10 17:01:45 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 Mon Oct 10 2011 at 17:01:45 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2822 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6187968 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): -8.768001 48.76300 ymin,ymax (A): -9.517000 38.19000 zmin,zma (A): -1.165000 54.55300 x,y,z range (A): 57.53100 47.70700 55.71800 scale (grids/A): 0.6187968 object centre (A): 19.99750 14.33650 26.69400 number of atom coordinates read : 2822 total number of charged atoms : 2681 net assigned charge : -2.499973 assigned positive charge : 422.9622 centred at (gu) : 89.02602 89.69411 89.33541 assigned negative charge : -425.4633 centred at (gu) : 88.94754 89.64480 89.31001 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7368 nv = 96 ne = 84 npr = 55888 no. pairs analyzed = 55888 no. exposed pairs = 3722 no. arc points = 26645 no. surface atoms = 1252 nbur = 1570 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 398 mr = 3857 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.3100000 number of dielectric boundary points 3876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2633 ## 271 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8976 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2110098E-09 -7.2704794E-11 midg,1,midg; midg,igrid,midg -5.7066627E-09 1.4843317E-09 1,midg,midg; igrid,midg,midg -9.2148174E-09 2.8922136E-09 gauss-seidel spectral radius is 0.9865049 estimated iterations to convergence 70 setup time was (sec) 0.6000000 now iterating at: 17:01:46 rms-change max change #iterations 0.1333980 20.39326 at 10iterations 1.2059676E-02 1.590502 at 20iterations 1.1071367E-03 0.1696692 at 30iterations 1.0367584E-04 1.4991760E-02 at 40iterations 1.0695914E-05 1.6269684E-03 at 50iterations finished qdiffx linear iterations at : 17:01:50 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 1.0695914E-05 1.6269684E-03 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.520000 DelPhi exited at 17:01:52 4.520u 0.400s 0:07.14 68.9% 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 17:01:52 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2822 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: 1.856390 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): -8.768001 48.76300 ymin,ymax (A): -9.517000 38.19000 zmin,zma (A): -1.165000 54.55300 x,y,z range (A): 57.53100 47.70700 55.71800 scale (grids/A): 1.856390 object centre (A): 19.99750 14.33650 26.69400 number of atom coordinates read : 2822 total number of charged atoms : 2681 net assigned charge : -2.499973 assigned positive charge : 422.9622 centred at (gu) : 87.07727 89.08185 88.00546 assigned negative charge : -425.4633 centred at (gu) : 86.84218 88.93393 87.92979 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 80039 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26645 grid for indexing accessible points = 1.400000 m= 27378 mr = 54189 m= 3924 mr = 19340 m= 178 mr = 2215 m= 2 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 349 time to turn everything in is 0.6500000 number of dielectric boundary points 35743 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 205 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 21043 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) : 0.6187968 object centre at (A) : 19.99750 14.33650 26.69400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2241404E-02 6.4443131E-03 midg,1,midg; midg,igrid,midg -1.8202899E-02 -2.2139039E-03 1,midg,midg; igrid,midg,midg -4.6317171E-02 3.1686399E-02 gauss-seidel spectral radius is 0.9985982 estimated iterations to convergence 212 setup time was (sec) 0.9700000 now iterating at: 17:01:54 rms-change max change #iterations 4.223435 208.4948 at 10iterations 1.956480 66.32013 at 20iterations 0.9040624 32.14386 at 30iterations 0.4179539 13.90188 at 40iterations 0.1938690 5.688847 at 50iterations 8.9683220E-02 2.907419 at 60iterations 4.1485861E-02 1.295667 at 70iterations 1.9265603E-02 0.6469030 at 80iterations 8.9222407E-03 0.2870674 at 90iterations 4.1325861E-03 0.1258850 at 100iterations 1.9172153E-03 6.0714722E-02 at 110iterations 8.8970887E-04 2.8082848E-02 at 120iterations finished qdiffx linear iterations at : 17:02:04 total time elapsed so far: 11.61000 # loops : 120 mean,max change (kT/e) : 8.8970887E-04 2.8082848E-02 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.77000 DelPhi exited at 17:02:05 11.776u 0.438s 0:12.55 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 Mon Oct 10 2011 at 17:02:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2822 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: 2.784586 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): -8.768001 48.76300 ymin,ymax (A): -9.517000 38.19000 zmin,zma (A): -1.165000 54.55300 x,y,z range (A): 57.53100 47.70700 55.71800 scale (grids/A): 2.784586 object centre (A): 19.99750 14.33650 26.69400 number of atom coordinates read : 2822 total number of charged atoms : 2681 net assigned charge : -2.499973 assigned positive charge : 422.9622 centred at (gu) : 85.61571 88.62262 87.00803 assigned negative charge : -425.4633 centred at (gu) : 85.26328 88.40084 86.89462 start vw surface at 0.1200000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 184884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26645 grid for indexing accessible points = 1.400000 m= 90227 mr = 131475 m= 30861 mr = 72404 m= 6859 mr = 23881 m= 801 mr = 4803 m= 27 mr = 410 m= 0 mr = 5 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 1082 time to turn everything in is 1.680000 number of dielectric boundary points 80681 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 21446 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) : 1.856390 object centre at (A) : 19.99750 14.33650 26.69400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1972083 -0.1788969 midg,1,midg; midg,igrid,midg -0.1636373 -4.7700640E-02 1,midg,midg; igrid,midg,midg -0.5648258 0.4775825 gauss-seidel spectral radius is 0.9992692 estimated iterations to convergence 292 setup time was (sec) 2.030000 now iterating at: 17:02:07 rms-change max change #iterations 10.30535 313.3964 at 10iterations 6.105146 156.6903 at 20iterations 3.592589 84.90691 at 30iterations 2.098390 46.63039 at 40iterations 1.224323 23.20498 at 50iterations 0.7117211 13.69253 at 60iterations 0.4129733 7.837349 at 70iterations 0.2394720 5.006520 at 80iterations 0.1386765 2.749168 at 90iterations 8.0003589E-02 1.523810 at 100iterations 4.6319056E-02 0.9075165 at 110iterations 2.6736479E-02 0.5061045 at 120iterations 1.5431671E-02 0.3198013 at 130iterations 8.9000771E-03 0.1689606 at 140iterations 5.1250202E-03 9.0518951E-02 at 150iterations 2.9597115E-03 5.3390503E-02 at 160iterations 1.7049635E-03 3.0736923E-02 at 170iterations 9.8313682E-04 1.8373489E-02 at 180iterations finished qdiffx linear iterations at : 17:02:25 total time elapsed so far: 19.57000 # loops : 180 mean,max change (kT/e) : 9.8313682E-04 1.8373489E-02 energy calculations done at 19.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.75000 DelPhi exited at 17:02:25 19.753u 0.467s 0:20.59 98.1% 0+0k 0+0io 0pf+0w