Mon Oct 10 14:04:13 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 14:04:13 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2147 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6714321 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): -19.18200 33.83900 ymin,ymax (A): -26.92000 20.17500 zmin,zma (A): -6.290000 41.96900 x,y,z range (A): 53.02100 47.09500 48.25900 scale (grids/A): 0.6714321 object centre (A): 7.328498 -3.372500 17.83950 number of atom coordinates read : 2147 total number of charged atoms : 2003 net assigned charge : -9.846986 assigned positive charge : 323.4398 centred at (gu) : 88.43928 91.63982 88.10440 assigned negative charge : -333.2870 centred at (gu) : 88.75108 91.69247 88.10736 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6574 nv = 96 ne = 84 npr = 44023 no. pairs analyzed = 44023 no. exposed pairs = 2714 no. arc points = 19415 no. surface atoms = 911 nbur = 1236 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 384 mr = 3579 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.3200000 number of dielectric boundary points 3323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1808 ## 148 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7528 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.9422198E-08 -2.4283759E-08 midg,1,midg; midg,igrid,midg -1.6668286E-08 -6.4695037E-08 1,midg,midg; igrid,midg,midg 4.7103523E-08 -7.7784797E-08 gauss-seidel spectral radius is 0.9884616 estimated iterations to convergence 76 setup time was (sec) 0.6200000 now iterating at: 14:04:14 rms-change max change #iterations 0.1687874 24.36911 at 10iterations 1.8123491E-02 2.515152 at 20iterations 2.0088861E-03 0.2857800 at 30iterations 2.2377232E-04 3.2657623E-02 at 40iterations 2.4540752E-05 3.5514832E-03 at 50iterations finished qdiffx linear iterations at : 14:04:18 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 2.4540752E-05 3.5514832E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 14:04:18 4.157u 0.247s 0:05.05 86.9% 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 14:04:19 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2147 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.014296 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): -19.18200 33.83900 ymin,ymax (A): -26.92000 20.17500 zmin,zma (A): -6.290000 41.96900 x,y,z range (A): 53.02100 47.09500 48.25900 scale (grids/A): 2.014296 object centre (A): 7.328498 -3.372500 17.83950 number of atom coordinates read : 2147 total number of charged atoms : 2003 net assigned charge : -9.846986 assigned positive charge : 323.4398 centred at (gu) : 85.31757 94.91930 84.31327 assigned negative charge : -333.2870 centred at (gu) : 86.25313 95.07745 84.32207 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 69662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19415 grid for indexing accessible points = 1.400000 m= 26288 mr = 47420 m= 4520 mr = 19694 m= 286 mr = 2882 m= 4 mr = 130 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 770 time to turn everything in is 0.6500000 number of dielectric boundary points 30634 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15829 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) : 0.6714321 object centre at (A) : 7.328498 -3.372500 17.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6125992E-02 -2.7515735E-02 midg,1,midg; midg,igrid,midg -1.3467246E-02 -2.1792915E-02 1,midg,midg; igrid,midg,midg 4.8239147E-03 -9.4143003E-02 gauss-seidel spectral radius is 0.9987269 estimated iterations to convergence 222 setup time was (sec) 0.9800000 now iterating at: 14:04:20 rms-change max change #iterations 4.309463 208.5626 at 10iterations 2.071211 77.15441 at 20iterations 0.9916857 35.39882 at 30iterations 0.4749381 15.34818 at 40iterations 0.2283850 8.036285 at 50iterations 0.1095045 3.718014 at 60iterations 5.2642260E-02 1.797685 at 70iterations 2.5289675E-02 0.7602448 at 80iterations 1.2133152E-02 0.4349174 at 90iterations 5.8329590E-03 0.1932206 at 100iterations 2.7963088E-03 8.2468674E-02 at 110iterations 1.3436937E-03 4.8350334E-02 at 120iterations finished qdiffx linear iterations at : 14:04:28 total time elapsed so far: 9.320000 # loops : 120 mean,max change (kT/e) : 1.3436937E-03 4.8350334E-02 energy calculations done at 9.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.500000 DelPhi exited at 14:04:29 9.506u 0.258s 0:10.13 96.2% 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 14:04:29 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2147 !!! WARNING: ASL 51 has a net charge of -0.1000 !!! WARNING: SEP 52 has a net charge of -0.4750 !!! 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: 3.021445 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): -19.18200 33.83900 ymin,ymax (A): -26.92000 20.17500 zmin,zma (A): -6.290000 41.96900 x,y,z range (A): 53.02100 47.09500 48.25900 scale (grids/A): 3.021445 object centre (A): 7.328498 -3.372500 17.83950 number of atom coordinates read : 2147 total number of charged atoms : 2003 net assigned charge : -9.846986 assigned positive charge : 323.4398 centred at (gu) : 82.97635 97.37900 81.46980 assigned negative charge : -333.2870 centred at (gu) : 84.37971 97.61616 81.48320 start vw surface at 0.1300000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 160881 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19415 grid for indexing accessible points = 1.400000 m= 82572 mr = 115022 m= 32325 mr = 67601 m= 8198 mr = 26517 m= 1195 mr = 6242 m= 79 mr = 810 m= 1 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 2699 time to turn everything in is 1.430000 number of dielectric boundary points 69019 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 16024 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) : 2.014296 object centre at (A) : 7.328498 -3.372500 17.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9533204E-02 -0.3072370 midg,1,midg; midg,igrid,midg -9.4909705E-02 -0.1547114 1,midg,midg; igrid,midg,midg 0.1539134 -0.8939987 gauss-seidel spectral radius is 0.9992766 estimated iterations to convergence 293 setup time was (sec) 1.790000 now iterating at: 14:04:31 rms-change max change #iterations 9.921467 429.1843 at 10iterations 5.769563 125.1216 at 20iterations 3.338921 64.86625 at 30iterations 1.934299 38.77170 at 40iterations 1.119037 21.89030 at 50iterations 0.6481489 13.52489 at 60iterations 0.3740039 6.996563 at 70iterations 0.2165733 4.202677 at 80iterations 0.1248504 2.482388 at 90iterations 7.2212070E-02 1.489853 at 100iterations 4.1665927E-02 0.7725906 at 110iterations 2.4107071E-02 0.4372644 at 120iterations 1.3888850E-02 0.2487183 at 130iterations 8.0283554E-03 0.1489506 at 140iterations 4.6324814E-03 8.7375164E-02 at 150iterations 2.6703479E-03 5.0540447E-02 at 160iterations 1.5457545E-03 2.6687622E-02 at 170iterations 8.9445052E-04 1.7364502E-02 at 180iterations finished qdiffx linear iterations at : 14:04:45 total time elapsed so far: 15.78000 # loops : 180 mean,max change (kT/e) : 8.9445052E-04 1.7364502E-02 energy calculations done at 15.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.00000 DelPhi exited at 14:04:46 16.002u 0.337s 0:16.84 96.9% 0+0k 0+0io 0pf+0w