Mon Oct 10 14:00:48 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 14:00:48 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 = 5414 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5314305 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): 15.53000 80.58000 ymin,ymax (A): 18.07100 84.72500 zmin,zma (A): 1.415000 68.40400 x,y,z range (A): 65.05000 66.65400 66.98900 scale (grids/A): 0.5314305 object centre (A): 48.05500 51.39800 34.90950 number of atom coordinates read : 5414 total number of charged atoms : 5249 net assigned charge : -1.499992 assigned positive charge : 812.4651 centred at (gu) : 90.51949 89.14777 90.53272 assigned negative charge : -813.9716 centred at (gu) : 90.41798 89.21725 90.64163 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 9856 nv = 96 ne = 84 npr = 108533 no. pairs analyzed = 108533 no. exposed pairs = 6929 no. arc points = 47807 no. surface atoms = 2318 nbur = 3096 mkacc time = 0.2500000 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 = 1.624000 m= 342 mr = 5076 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.5300000 number of dielectric boundary points 5106 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4821 ## 655 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 13100 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0252003E-10 -9.4483599E-10 midg,1,midg; midg,igrid,midg 5.2880039E-10 -4.3650000E-10 1,midg,midg; igrid,midg,midg -6.7425565E-10 7.3378581E-10 gauss-seidel spectral radius is 0.9819385 estimated iterations to convergence 61 setup time was (sec) 0.7700000 now iterating at: 14:00:49 rms-change max change #iterations 8.8228442E-02 12.96964 at 10iterations 5.8473591E-03 0.7534142 at 20iterations 6.7655987E-04 0.1318779 at 30iterations 1.8504659E-04 3.9783478E-02 at 40iterations 6.0437254E-05 1.2516022E-02 at 50iterations finished qdiffx linear iterations at : 14:00:51 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 6.0437254E-05 1.2516022E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 14:00:52 3.597u 0.213s 0:04.28 88.7% 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 14:00:52 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 = 5414 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.2400000 grid size : 179 scale,in grids/A, set to be: 1.594292 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): 15.53000 80.58000 ymin,ymax (A): 18.07100 84.72500 zmin,zma (A): 1.415000 68.40400 x,y,z range (A): 65.05000 66.65400 66.98900 scale (grids/A): 1.594292 object centre (A): 48.05500 51.39800 34.90950 number of atom coordinates read : 5414 total number of charged atoms : 5249 net assigned charge : -1.499992 assigned positive charge : 812.4651 centred at (gu) : 91.55704 87.44157 91.59669 assigned negative charge : -813.9716 centred at (gu) : 91.25369 87.65173 91.92436 start vw surface at 0.3600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 110181 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47807 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 33390 mr = 75564 m= 3135 mr = 22332 m= 78 mr = 1414 m= 0 mr = 7 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 462 time to turn everything in is 0.9100000 number of dielectric boundary points 47467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 614 ## 7 charges are in solution ## iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 39901 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) : 0.5314305 object centre at (A) : 48.05500 51.39800 34.90950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3049137E-02 -5.0705727E-02 midg,1,midg; midg,igrid,midg -4.2913854E-03 -2.3031384E-02 1,midg,midg; igrid,midg,midg -1.9933851E-03 2.0920444E-02 gauss-seidel spectral radius is 0.9983402 estimated iterations to convergence 195 setup time was (sec) 1.230000 now iterating at: 14:00:54 rms-change max change #iterations 4.477357 165.8740 at 10iterations 1.935541 60.31879 at 20iterations 0.8380530 23.69026 at 30iterations 0.3624305 10.53238 at 40iterations 0.1572918 4.353577 at 50iterations 6.8332039E-02 2.019094 at 60iterations 2.9700249E-02 0.8869610 at 70iterations 1.2924739E-02 0.3794556 at 80iterations 5.6477147E-03 0.1693764 at 90iterations 2.4791558E-03 7.2784424E-02 at 100iterations 1.1066195E-03 3.2191277E-02 at 110iterations 5.0895929E-04 1.5594482E-02 at 120iterations finished qdiffx linear iterations at : 14:01:02 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 5.0895929E-04 1.5594482E-02 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.380000 DelPhi exited at 14:01:02 9.385u 0.236s 0:10.31 93.2% 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 14:01:02 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 = 5414 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.391438 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): 15.53000 80.58000 ymin,ymax (A): 18.07100 84.72500 zmin,zma (A): 1.415000 68.40400 x,y,z range (A): 65.05000 66.65400 66.98900 scale (grids/A): 2.391438 object centre (A): 48.05500 51.39800 34.90950 number of atom coordinates read : 5414 total number of charged atoms : 5249 net assigned charge : -1.499992 assigned positive charge : 812.4651 centred at (gu) : 92.33482 86.16207 92.39465 assigned negative charge : -813.9716 centred at (gu) : 91.88059 86.47756 92.88640 start vw surface at 0.2100000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 256481 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47807 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 117710 mr = 185703 m= 31554 mr = 91956 m= 4736 mr = 23018 m= 302 mr = 2979 m= 4 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 1549 time to turn everything in is 1.920000 number of dielectric boundary points 107015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 51 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 41920 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) : 1.594292 object centre at (A) : 48.05500 51.39800 34.90950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1710415 -1.077376 midg,1,midg; midg,igrid,midg -0.2888062 -0.3865536 1,midg,midg; igrid,midg,midg 0.1588445 0.4809742 gauss-seidel spectral radius is 0.9992514 estimated iterations to convergence 288 setup time was (sec) 2.260000 now iterating at: 14:01:05 rms-change max change #iterations 11.83230 307.0926 at 10iterations 7.059853 163.0882 at 20iterations 4.171390 79.30939 at 30iterations 2.458398 49.31811 at 40iterations 1.436827 33.10465 at 50iterations 0.8386563 19.23452 at 60iterations 0.4871599 8.901321 at 70iterations 0.2825823 5.005558 at 80iterations 0.1638708 2.938807 at 90iterations 9.4710313E-02 1.885855 at 100iterations 5.4702077E-02 0.9700978 at 110iterations 3.1586714E-02 0.5337830 at 120iterations 1.8230198E-02 0.3316269 at 130iterations 1.0520936E-02 0.1800995 at 140iterations 6.0516703E-03 0.1006553 at 150iterations 3.4996388E-03 5.7324409E-02 at 160iterations 2.0188417E-03 3.3396721E-02 at 170iterations 1.1709754E-03 1.9666672E-02 at 180iterations finished qdiffx linear iterations at : 14:01:17 total time elapsed so far: 13.87000 # loops : 180 mean,max change (kT/e) : 1.1709754E-03 1.9666672E-02 energy calculations done at 13.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.05000 DelPhi exited at 14:01:17 14.047u 0.273s 0:14.81 96.6% 0+0k 0+0io 0pf+0w