Sun Oct 9 03:52:24 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+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 Sun Oct 9 2011 at 03:52:24 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5383 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: 0.4342099 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): 2.672000 73.47500 ymin,ymax (A): -10.52100 48.03500 zmin,zma (A): -8.271000 73.71700 x,y,z range (A): 70.80300 58.55600 81.98801 scale (grids/A): 0.4342099 object centre (A): 38.07350 18.75700 32.72300 number of atom coordinates read : 5383 total number of charged atoms : 5141 net assigned charge : 16.49999 assigned positive charge : 801.9131 centred at (gu) : 88.66107 90.72756 87.56322 assigned negative charge : -785.4202 centred at (gu) : 88.62436 90.76383 87.53232 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6024 nv = 96 ne = 84 npr = 108530 no. pairs analyzed = 108530 no. exposed pairs = 6708 no. arc points = 47109 no. surface atoms = 2253 nbur = 3130 mkacc time = 0.1900000 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 = 1.932000 m= 145 mr = 2924 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3245 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3871 ## 859 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8264 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.0814548E-12 3.0081944E-12 midg,1,midg; midg,igrid,midg 5.2545542E-12 2.6540211E-12 1,midg,midg; igrid,midg,midg 3.1289210E-12 4.3934817E-12 gauss-seidel spectral radius is 0.9729972 estimated iterations to convergence 51 setup time was (sec) 0.5100000 now iterating at: 03:52:25 rms-change max change #iterations 3.0591903E-02 5.941437 at 10iterations 3.0771492E-03 0.6368980 at 20iterations 8.2768966E-04 0.1603775 at 30iterations 2.3676103E-04 4.4048309E-02 at 40iterations 6.9004571E-05 1.2474060E-02 at 50iterations finished qdiffx linear iterations at : 03:52:28 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 6.9004571E-05 1.2474060E-02 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 03:52:28 3.609u 0.192s 0:04.13 91.7% 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 Sun Oct 9 2011 at 03:52:28 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5383 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: 1.302630 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): 2.672000 73.47500 ymin,ymax (A): -10.52100 48.03500 zmin,zma (A): -8.271000 73.71700 x,y,z range (A): 70.80300 58.55600 81.98801 scale (grids/A): 1.302630 object centre (A): 38.07350 18.75700 32.72300 number of atom coordinates read : 5383 total number of charged atoms : 5141 net assigned charge : 16.49999 assigned positive charge : 801.9131 centred at (gu) : 85.98090 92.18101 82.68777 assigned negative charge : -785.4202 centred at (gu) : 85.87271 92.29082 82.59667 start vw surface at 0.1400000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 71560 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47109 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.820000 m= 16003 mr = 47703 m= 788 mr = 9491 m= 6 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 388 time to turn everything in is 0.3700000 number of dielectric boundary points 30983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 862 ## 28 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 35775 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) : 0.4342099 object centre at (A) : 38.07350 18.75700 32.72300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.0317175E-03 1.7953393E-03 midg,1,midg; midg,igrid,midg 1.9953854E-03 1.9833934E-03 1,midg,midg; igrid,midg,midg 1.0730227E-02 7.0241657E-03 gauss-seidel spectral radius is 0.9973319 estimated iterations to convergence 154 setup time was (sec) 0.5900000 now iterating at: 03:52:29 rms-change max change #iterations 2.676995 138.9316 at 10iterations 0.9235448 40.13221 at 20iterations 0.3215916 13.60599 at 30iterations 0.1122349 4.598114 at 40iterations 3.9354362E-02 1.491901 at 50iterations 1.4178054E-02 0.6543713 at 60iterations 5.4850513E-03 0.2006544 at 70iterations 2.4541784E-03 9.5489502E-02 at 80iterations 1.3063293E-03 4.6356201E-02 at 90iterations 7.8249659E-04 2.5337219E-02 at 100iterations 4.9519638E-04 1.5872955E-02 at 110iterations 3.1883983E-04 1.0128021E-02 at 120iterations finished qdiffx linear iterations at : 03:52:36 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 3.1883983E-04 1.0128021E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 03:52:36 7.683u 0.185s 0:08.25 95.2% 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 Sun Oct 9 2011 at 03:52:37 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: 321 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5383 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: 1.953944 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): 2.672000 73.47500 ymin,ymax (A): -10.52100 48.03500 zmin,zma (A): -8.271000 73.71700 x,y,z range (A): 70.80300 58.55600 81.98801 scale (grids/A): 1.953944 object centre (A): 38.07350 18.75700 32.72300 number of atom coordinates read : 5383 total number of charged atoms : 5141 net assigned charge : 16.49999 assigned positive charge : 801.9131 centred at (gu) : 83.97098 93.27113 79.03109 assigned negative charge : -785.4202 centred at (gu) : 83.80904 93.43609 78.89491 start vw surface at 0.1300000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 168590 reading accessible surface arcs data from file ARCDAT no. of arc points read = 47109 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.792000 m= 63597 mr = 119545 m= 10841 mr = 47137 m= 799 mr = 6769 m= 16 mr = 318 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 1251 time to turn everything in is 0.8300000 number of dielectric boundary points 70074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 255 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 40551 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) : 1.302630 object centre at (A) : 38.07350 18.75700 32.72300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2713504 4.9536679E-02 midg,1,midg; midg,igrid,midg 4.9569778E-02 5.0360058E-02 1,midg,midg; igrid,midg,midg 0.3509238 0.2244981 gauss-seidel spectral radius is 0.9989201 estimated iterations to convergence 241 setup time was (sec) 1.060000 now iterating at: 03:52:38 rms-change max change #iterations 8.104132 251.2012 at 10iterations 4.270436 114.4212 at 20iterations 2.236959 56.67226 at 30iterations 1.170011 26.97997 at 40iterations 0.6074505 15.10508 at 50iterations 0.3145402 7.497938 at 60iterations 0.1628705 4.538127 at 70iterations 8.3890751E-02 2.023268 at 80iterations 4.3287579E-02 1.002677 at 90iterations 2.2316623E-02 0.4819183 at 100iterations 1.1526614E-02 0.2745056 at 110iterations 5.9999386E-03 0.1291513 at 120iterations 3.1572541E-03 7.1632385E-02 at 130iterations 1.6930744E-03 3.7555695E-02 at 140iterations 9.3829603E-04 1.9618988E-02 at 150iterations 5.4692634E-04 1.1886597E-02 at 160iterations 3.3955512E-04 7.9307556E-03 at 170iterations 2.2363731E-04 4.6310425E-03 at 180iterations finished qdiffx linear iterations at : 03:52:49 total time elapsed so far: 12.11000 # loops : 180 mean,max change (kT/e) : 2.2363731E-04 4.6310425E-03 energy calculations done at 12.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 03:52:49 12.237u 0.226s 0:12.72 97.8% 0+0k 0+0io 0pf+0w