Mon Oct 10 11:19:30 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 Mon Oct 10 2011 at 11:19:30 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 0.7469576 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): -20.91300 24.64100 ymin,ymax (A): -8.183001 36.21300 zmin,zma (A): -3.494000 44.16600 x,y,z range (A): 45.55400 44.39600 47.66000 scale (grids/A): 0.7469576 object centre (A): 1.863999 14.01500 20.33600 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.8999 centred at (gu) : 88.83556 90.47353 90.24422 assigned negative charge : -324.1720 centred at (gu) : 88.85439 90.56042 90.42587 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8152 nv = 96 ne = 84 npr = 43649 no. pairs analyzed = 43649 no. exposed pairs = 2774 no. arc points = 19231 no. surface atoms = 934 nbur = 1183 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 604 mr = 4500 m= 6 mr = 121 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 4141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1501 ## 113 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8533 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.9916788E-08 -3.6178793E-07 midg,1,midg; midg,igrid,midg -2.3655355E-08 -2.5175606E-07 1,midg,midg; igrid,midg,midg -1.2887720E-07 -1.2128370E-07 gauss-seidel spectral radius is 0.9906607 estimated iterations to convergence 84 setup time was (sec) 0.5500000 now iterating at: 11:19:31 rms-change max change #iterations 0.2572307 34.63216 at 10iterations 3.5075702E-02 4.344996 at 20iterations 4.7705327E-03 0.5758228 at 30iterations 6.6013291E-04 8.4617615E-02 at 40iterations 8.9928493E-05 1.1091232E-02 at 50iterations finished qdiffx linear iterations at : 11:19:34 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 8.9928493E-05 1.1091232E-02 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 11:19:35 4.426u 0.384s 0:05.11 93.9% 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 11:19:35 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 2.240873 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): -20.91300 24.64100 ymin,ymax (A): -8.183001 36.21300 zmin,zma (A): -3.494000 44.16600 x,y,z range (A): 45.55400 44.39600 47.66000 scale (grids/A): 2.240873 object centre (A): 1.863999 14.01500 20.33600 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.8999 centred at (gu) : 86.50678 91.42043 90.73281 assigned negative charge : -324.1720 centred at (gu) : 86.56310 91.68126 91.27763 start vw surface at 0.1200000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 85655 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19231 grid for indexing accessible points = 1.400000 m= 34384 mr = 58930 m= 7346 mr = 25948 m= 819 mr = 5089 m= 26 mr = 431 m= 0 mr = 6 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 37826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 40 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 15769 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) : 0.7469576 object centre at (A) : 1.863999 14.01500 20.33600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4473326E-03 -0.1398670 midg,1,midg; midg,igrid,midg -2.6305558E-02 -3.4553055E-02 1,midg,midg; igrid,midg,midg -2.1181693E-02 -5.1810020E-03 gauss-seidel spectral radius is 0.9989443 estimated iterations to convergence 243 setup time was (sec) 1.020000 now iterating at: 11:19:36 rms-change max change #iterations 5.169959 193.8322 at 10iterations 2.640844 84.66946 at 20iterations 1.351060 40.08228 at 30iterations 0.6926346 20.25296 at 40iterations 0.3556169 10.15421 at 50iterations 0.1822306 5.807188 at 60iterations 9.3352161E-02 2.720562 at 70iterations 4.7750425E-02 1.246878 at 80iterations 2.4494013E-02 0.6458659 at 90iterations 1.2578800E-02 0.3249359 at 100iterations 6.4610378E-03 0.1918182 at 110iterations 3.3047900E-03 0.1049085 at 120iterations finished qdiffx linear iterations at : 11:19:46 total time elapsed so far: 10.67000 # loops : 120 mean,max change (kT/e) : 3.3047900E-03 0.1049085 energy calculations done at 10.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.83000 DelPhi exited at 11:19:46 10.832u 0.445s 0:11.58 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 Mon Oct 10 2011 at 11:19:46 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: 244 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2117 !!! WARNING: LYS 224 has a net charge of -0.2720 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: 3.361309 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): -20.91300 24.64100 ymin,ymax (A): -8.183001 36.21300 zmin,zma (A): -3.494000 44.16600 x,y,z range (A): 45.55400 44.39600 47.66000 scale (grids/A): 3.361309 object centre (A): 1.863999 14.01500 20.33600 number of atom coordinates read : 2117 total number of charged atoms : 1978 net assigned charge : -6.271980 assigned positive charge : 317.8999 centred at (gu) : 84.76022 92.13063 91.09919 assigned negative charge : -324.1720 centred at (gu) : 84.84473 92.52196 91.91649 start vw surface at 0.1100000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 196922 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19231 grid for indexing accessible points = 1.400000 m= 105220 mr = 141755 m= 45093 mr = 87059 m= 14195 mr = 37241 m= 3121 mr = 11062 m= 424 mr = 2394 m= 22 mr = 271 m= 0 mr = 4 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.250000 number of dielectric boundary points 85211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.390000 number of grid points assigned charge 15824 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) : 2.240873 object centre at (A) : 1.863999 14.01500 20.33600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3175063E-02 -1.174159 midg,1,midg; midg,igrid,midg -0.2376084 -0.1679005 1,midg,midg; igrid,midg,midg -0.2237624 -0.1565481 gauss-seidel spectral radius is 0.9993247 estimated iterations to convergence 304 setup time was (sec) 2.590000 now iterating at: 11:19:49 rms-change max change #iterations 11.21530 271.0168 at 10iterations 6.640276 127.3688 at 20iterations 3.942343 73.00911 at 30iterations 2.325582 44.31937 at 40iterations 1.376094 23.64207 at 50iterations 0.8123884 13.96407 at 60iterations 0.4786734 7.645653 at 70iterations 0.2831950 4.819099 at 80iterations 0.1664137 2.581562 at 90iterations 9.8176718E-02 1.875315 at 100iterations 5.7654731E-02 0.9217682 at 110iterations 3.4036342E-02 0.5502510 at 120iterations 2.0008728E-02 0.3066683 at 130iterations 1.1770868E-02 0.1892209 at 140iterations 6.9478084E-03 0.1063266 at 150iterations 4.0864693E-03 6.1948299E-02 at 160iterations 2.4121676E-03 4.0475845E-02 at 170iterations 1.4172680E-03 2.1701336E-02 at 180iterations finished qdiffx linear iterations at : 11:20:07 total time elapsed so far: 19.86000 # loops : 180 mean,max change (kT/e) : 1.4172680E-03 2.1701336E-02 energy calculations done at 19.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.01000 DelPhi exited at 11:20:07 20.017u 0.498s 0:20.80 98.5% 0+0k 0+0io 0pf+0w