Sun Oct 16 15:02:33 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 16 2011 at 15:02:33 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 = 2893 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6203063 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): 14.11400 71.50500 ymin,ymax (A): 4.319000 51.78500 zmin,zma (A): 7.626000 63.62800 x,y,z range (A): 57.39101 47.46600 56.00200 scale (grids/A): 0.6203063 object centre (A): 42.80950 28.05200 35.62700 number of atom coordinates read : 2893 total number of charged atoms : 2752 net assigned charge : -1.999967 assigned positive charge : 433.1981 centred at (gu) : 89.01653 90.24539 90.90054 assigned negative charge : -435.1992 centred at (gu) : 88.94967 90.32722 90.93881 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7523 nv = 96 ne = 84 npr = 57600 no. pairs analyzed = 57600 no. exposed pairs = 3842 no. arc points = 27340 no. surface atoms = 1309 nbur = 1584 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3908 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 24 time to turn everything in is 0.2300000 number of dielectric boundary points 3975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2666 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9147 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0848910E-09 -5.3730873E-09 midg,1,midg; midg,igrid,midg 4.3208295E-09 -8.1489029E-09 1,midg,midg; igrid,midg,midg -8.1856033E-09 2.7671754E-09 gauss-seidel spectral radius is 0.9865748 estimated iterations to convergence 71 setup time was (sec) 0.4900000 now iterating at: 15:02:34 rms-change max change #iterations 0.1320513 19.88434 at 10iterations 1.2022454E-02 1.604995 at 20iterations 1.1131520E-03 0.1527443 at 30iterations 1.0428412E-04 1.3959885E-02 at 40iterations 1.0652229E-05 1.5200377E-03 at 50iterations finished qdiffx linear iterations at : 15:02:38 total time elapsed so far: 4.310000 # loops : 50 mean,max change (kT/e) : 1.0652229E-05 1.5200377E-03 energy calculations done at 4.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 15:02:38 4.442u 0.320s 0:05.03 94.6% 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 16 2011 at 15:02:38 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 = 2893 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.860919 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): 14.11400 71.50500 ymin,ymax (A): 4.319000 51.78500 zmin,zma (A): 7.626000 63.62800 x,y,z range (A): 57.39101 47.46600 56.00200 scale (grids/A): 1.860919 object centre (A): 42.80950 28.05200 35.62700 number of atom coordinates read : 2893 total number of charged atoms : 2752 net assigned charge : -1.999967 assigned positive charge : 433.1981 centred at (gu) : 87.04836 90.73540 92.70091 assigned negative charge : -435.1992 centred at (gu) : 86.84860 90.98127 92.81605 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27340 grid for indexing accessible points = 1.400000 m= 28237 mr = 54318 m= 4168 mr = 20087 m= 245 mr = 2464 m= 0 mr = 81 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 567 time to turn everything in is 0.4300000 number of dielectric boundary points 36646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 21580 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) : 0.6203063 object centre at (A) : 42.80950 28.05200 35.62700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1445043E-03 1.2182986E-02 midg,1,midg; midg,igrid,midg 6.6197421E-03 -1.8465573E-02 1,midg,midg; igrid,midg,midg -5.7204187E-02 2.4428241E-02 gauss-seidel spectral radius is 0.9986121 estimated iterations to convergence 213 setup time was (sec) 0.7400000 now iterating at: 15:02:39 rms-change max change #iterations 4.323140 184.7339 at 10iterations 1.999786 69.93863 at 20iterations 0.9293479 30.27840 at 30iterations 0.4304198 15.76193 at 40iterations 0.2003615 5.901158 at 50iterations 9.3054555E-02 3.057931 at 60iterations 4.3254916E-02 1.302806 at 70iterations 2.0058161E-02 0.6923752 at 80iterations 9.3455892E-03 0.2752762 at 90iterations 4.3527423E-03 0.1262856 at 100iterations 2.0279554E-03 6.5399170E-02 at 110iterations 9.4097399E-04 2.8364182E-02 at 120iterations finished qdiffx linear iterations at : 15:02:49 total time elapsed so far: 10.44000 # loops : 120 mean,max change (kT/e) : 9.4097399E-04 2.8364182E-02 energy calculations done at 10.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.58000 DelPhi exited at 15:02:49 10.579u 0.365s 0:11.22 97.4% 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 Sun Oct 16 2011 at 15:02:49 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 = 2893 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.791378 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): 14.11400 71.50500 ymin,ymax (A): 4.319000 51.78500 zmin,zma (A): 7.626000 63.62800 x,y,z range (A): 57.39101 47.46600 56.00200 scale (grids/A): 2.791378 object centre (A): 42.80950 28.05200 35.62700 number of atom coordinates read : 2893 total number of charged atoms : 2752 net assigned charge : -1.999967 assigned positive charge : 433.1981 centred at (gu) : 85.57256 91.10275 94.05119 assigned negative charge : -435.1992 centred at (gu) : 85.27287 91.47194 94.22390 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 187151 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27340 grid for indexing accessible points = 1.400000 m= 91990 mr = 132225 m= 32105 mr = 73763 m= 7513 mr = 25101 m= 1015 mr = 5498 m= 72 mr = 605 m= 0 mr = 31 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 2111 time to turn everything in is 1.150000 number of dielectric boundary points 82623 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 22015 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) : 1.860919 object centre at (A) : 42.80950 28.05200 35.62700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3415077 0.2288014 midg,1,midg; midg,igrid,midg 7.6182194E-02 -0.1860871 1,midg,midg; igrid,midg,midg -0.6546130 0.3851318 gauss-seidel spectral radius is 0.9992757 estimated iterations to convergence 293 setup time was (sec) 1.490000 now iterating at: 15:02:51 rms-change max change #iterations 10.45425 305.8158 at 10iterations 6.247561 174.3554 at 20iterations 3.689558 81.29620 at 30iterations 2.173155 47.93222 at 40iterations 1.270949 25.79652 at 50iterations 0.7443584 14.45597 at 60iterations 0.4331784 8.547920 at 70iterations 0.2517452 4.579149 at 80iterations 0.1461403 2.596287 at 90iterations 8.4756941E-02 1.501178 at 100iterations 4.9203239E-02 0.9582672 at 110iterations 2.8493825E-02 0.5355053 at 120iterations 1.6512884E-02 0.2937622 at 130iterations 9.5661264E-03 0.1799803 at 140iterations 5.5355416E-03 0.1077833 at 150iterations 3.1976828E-03 5.9127808E-02 at 160iterations 1.8469869E-03 3.4127235E-02 at 170iterations 1.0665136E-03 1.7839432E-02 at 180iterations finished qdiffx linear iterations at : 15:03:07 total time elapsed so far: 17.42000 # loops : 180 mean,max change (kT/e) : 1.0665136E-03 1.7839432E-02 energy calculations done at 17.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.55000 DelPhi exited at 15:03:08 17.555u 0.387s 0:18.24 98.3% 0+0k 0+0io 0pf+0w