Sun Oct 9 01:49:05 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 01:49:05 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3290 !!! WARNING: HIT 84 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5717865 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): -24.23900 37.61700 ymin,ymax (A): 20.39000 79.70300 zmin,zma (A): -30.42100 31.84000 x,y,z range (A): 61.85600 59.31300 62.26100 scale (grids/A): 0.5717865 object centre (A): 6.689000 50.04650 0.7095003 number of atom coordinates read : 3290 total number of charged atoms : 3146 net assigned charge : 12.51404 assigned positive charge : 486.5016 centred at (gu) : 91.74876 89.57056 88.15614 assigned negative charge : -473.9893 centred at (gu) : 91.81442 89.35970 88.06764 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7486 nv = 96 ne = 84 npr = 62854 no. pairs analyzed = 62854 no. exposed pairs = 4551 no. arc points = 32615 no. surface atoms = 1513 nbur = 1777 mkacc time = 0.1600000 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 = 1.512000 m= 356 mr = 3732 m= 4 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3359 ## 404 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9425 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.6202622E-10 2.3812217E-09 midg,1,midg; midg,igrid,midg -1.9079303E-09 5.1834386E-09 1,midg,midg; igrid,midg,midg 2.1733195E-09 1.3773670E-09 gauss-seidel spectral radius is 0.9842610 estimated iterations to convergence 65 setup time was (sec) 0.6700000 now iterating at: 01:49:06 rms-change max change #iterations 9.6002758E-02 14.01157 at 10iterations 7.1190824E-03 1.186308 at 20iterations 5.6724966E-04 7.9498291E-02 at 30iterations 5.8873167E-05 1.1730194E-02 at 40iterations 1.2129413E-05 3.0307770E-03 at 50iterations finished qdiffx linear iterations at : 01:49:10 total time elapsed so far: 4.360000 # loops : 50 mean,max change (kT/e) : 1.2129413E-05 3.0307770E-03 energy calculations done at 4.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 01:49:11 4.539u 0.389s 0:05.21 94.2% 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 01:49:11 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3290 !!! WARNING: HIT 84 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.715359 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): -24.23900 37.61700 ymin,ymax (A): 20.39000 79.70300 zmin,zma (A): -30.42100 31.84000 x,y,z range (A): 61.85600 59.31300 62.26100 scale (grids/A): 1.715359 object centre (A): 6.689000 50.04650 0.7095003 number of atom coordinates read : 3290 total number of charged atoms : 3146 net assigned charge : 12.51404 assigned positive charge : 486.5016 centred at (gu) : 95.24515 88.71085 84.46762 assigned negative charge : -473.9893 centred at (gu) : 95.44299 88.07901 84.20272 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81731 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32615 grid for indexing accessible points = 1.400000 m= 27638 mr = 53949 m= 3600 mr = 19171 m= 134 mr = 1944 m= 3 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 904 time to turn everything in is 0.6800000 number of dielectric boundary points 38012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 351 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 24388 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) : 0.5717865 object centre at (A) : 6.689000 50.04650 0.7095003 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7271166E-02 4.9456537E-02 midg,1,midg; midg,igrid,midg -1.8880811E-02 1.6681626E-02 1,midg,midg; igrid,midg,midg 9.3743233E-03 1.8622672E-02 gauss-seidel spectral radius is 0.9984133 estimated iterations to convergence 199 setup time was (sec) 0.9800000 now iterating at: 01:49:12 rms-change max change #iterations 3.865497 215.2154 at 10iterations 1.685528 62.42244 at 20iterations 0.7423884 23.66741 at 30iterations 0.3268186 10.33941 at 40iterations 0.1441474 4.557959 at 50iterations 6.3419379E-02 2.109192 at 60iterations 2.7999870E-02 0.9001656 at 70iterations 1.2311685E-02 0.4575100 at 80iterations 5.4509272E-03 0.1724243 at 90iterations 2.4082353E-03 7.7288628E-02 at 100iterations 1.0678279E-03 3.4978986E-02 at 110iterations 4.7134407E-04 1.5237808E-02 at 120iterations finished qdiffx linear iterations at : 01:49:21 total time elapsed so far: 10.52000 # loops : 120 mean,max change (kT/e) : 4.7134407E-04 1.5237808E-02 energy calculations done at 10.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.67000 DelPhi exited at 01:49:22 10.679u 0.458s 0:11.42 97.3% 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 01:49:22 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3290 !!! WARNING: HIT 84 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.573039 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): -24.23900 37.61700 ymin,ymax (A): 20.39000 79.70300 zmin,zma (A): -30.42100 31.84000 x,y,z range (A): 61.85600 59.31300 62.26100 scale (grids/A): 2.573039 object centre (A): 6.689000 50.04650 0.7095003 number of atom coordinates read : 3290 total number of charged atoms : 3146 net assigned charge : 12.51404 assigned positive charge : 486.5016 centred at (gu) : 97.86758 88.06613 81.70123 assigned negative charge : -473.9893 centred at (gu) : 98.16440 87.11852 81.30397 start vw surface at 0.1400000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 189240 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32615 grid for indexing accessible points = 1.400000 m= 91440 mr = 132161 m= 29926 mr = 72033 m= 6043 mr = 22865 m= 615 mr = 4140 m= 13 mr = 327 m= 0 mr = 2 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 2739 time to turn everything in is 1.690000 number of dielectric boundary points 85749 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 25158 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) : 1.715359 object centre at (A) : 6.689000 50.04650 0.7095003 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4284966 0.7269295 midg,1,midg; midg,igrid,midg -0.1742636 0.2229013 1,midg,midg; igrid,midg,midg 3.4496117E-02 0.1802281 gauss-seidel spectral radius is 0.9992241 estimated iterations to convergence 283 setup time was (sec) 2.030000 now iterating at: 01:49:25 rms-change max change #iterations 9.876714 312.6618 at 10iterations 5.774227 140.1557 at 20iterations 3.351587 78.19894 at 30iterations 1.929814 41.41166 at 40iterations 1.109073 21.48092 at 50iterations 0.6344339 11.92002 at 60iterations 0.3628136 7.281277 at 70iterations 0.2074252 4.224201 at 80iterations 0.1178775 2.521004 at 90iterations 6.7087293E-02 1.201656 at 100iterations 3.8215388E-02 0.7339630 at 110iterations 2.1705145E-02 0.3822308 at 120iterations 1.2355819E-02 0.2439866 at 130iterations 6.9992072E-03 0.1284714 at 140iterations 3.9732209E-03 6.9084167E-02 at 150iterations 2.2573639E-03 4.1671753E-02 at 160iterations 1.2832070E-03 2.3772478E-02 at 170iterations 7.2937086E-04 1.4440298E-02 at 180iterations finished qdiffx linear iterations at : 01:49:41 total time elapsed so far: 18.82000 # loops : 180 mean,max change (kT/e) : 7.2937086E-04 1.4440298E-02 energy calculations done at 18.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.99000 DelPhi exited at 01:49:42 18.993u 0.497s 0:19.77 98.5% 0+0k 0+0io 0pf+0w