Mon Oct 10 13:56:16 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 13:56:17 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2335 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: GLM 85 has a net charge of -0.0940 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: 0.6357256 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): -27.16800 25.59700 ymin,ymax (A): 7.763000 48.70100 zmin,zma (A): -13.09600 42.90300 x,y,z range (A): 52.76500 40.93800 55.99900 scale (grids/A): 0.6357256 object centre (A): -0.7854996 28.23200 14.90350 number of atom coordinates read : 2335 total number of charged atoms : 2197 net assigned charge : 7.920017 assigned positive charge : 341.1985 centred at (gu) : 91.02740 90.97825 91.07574 assigned negative charge : -333.2791 centred at (gu) : 90.94222 90.89156 91.05993 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6371 nv = 96 ne = 84 npr = 47488 no. pairs analyzed = 47488 no. exposed pairs = 3187 no. arc points = 22215 no. surface atoms = 1064 nbur = 1271 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3209 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2143 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 7606 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.8780177E-09 1.4267676E-08 midg,1,midg; midg,igrid,midg 1.8712014E-09 2.1705869E-08 1,midg,midg; igrid,midg,midg 1.9661226E-09 2.1770598E-08 gauss-seidel spectral radius is 0.9871647 estimated iterations to convergence 72 setup time was (sec) 0.6600000 now iterating at: 13:56:17 rms-change max change #iterations 0.1332054 21.85442 at 10iterations 1.2886838E-02 2.197798 at 20iterations 1.2976277E-03 0.2068501 at 30iterations 1.3683151E-04 2.1995544E-02 at 40iterations 1.8848576E-05 3.0384064E-03 at 50iterations finished qdiffx linear iterations at : 13:56:21 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 1.8848576E-05 3.0384064E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 13:56:21 4.120u 0.195s 0:04.77 90.3% 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 13:56:21 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2335 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: GLM 85 has a net charge of -0.0940 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: 1.907177 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): -27.16800 25.59700 ymin,ymax (A): 7.763000 48.70100 zmin,zma (A): -13.09600 42.90300 x,y,z range (A): 52.76500 40.93800 55.99900 scale (grids/A): 1.907177 object centre (A): -0.7854996 28.23200 14.90350 number of atom coordinates read : 2335 total number of charged atoms : 2197 net assigned charge : 7.920017 assigned positive charge : 341.1985 centred at (gu) : 93.08189 92.93450 93.22704 assigned negative charge : -333.2791 centred at (gu) : 92.82688 92.67465 93.18010 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 67719 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22215 grid for indexing accessible points = 1.400000 m= 23190 mr = 44673 m= 3453 mr = 16039 m= 218 mr = 1898 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 31926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 17298 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) : 0.6357256 object centre at (A) : -0.7854996 28.23200 14.90350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1267084E-02 2.8024051E-02 midg,1,midg; midg,igrid,midg -3.0327577E-03 2.3739252E-02 1,midg,midg; igrid,midg,midg 2.8033338E-02 4.6115696E-02 gauss-seidel spectral radius is 0.9986187 estimated iterations to convergence 213 setup time was (sec) 0.9900000 now iterating at: 13:56:23 rms-change max change #iterations 3.956828 184.5447 at 10iterations 1.838598 62.22679 at 20iterations 0.8586922 32.39795 at 30iterations 0.3992441 12.62337 at 40iterations 0.1852164 6.479966 at 50iterations 8.6555503E-02 3.150132 at 60iterations 4.0175818E-02 1.473092 at 70iterations 1.8693116E-02 0.5909715 at 80iterations 8.7366188E-03 0.2851563 at 90iterations 4.0641660E-03 0.1265259 at 100iterations 1.8946815E-03 6.2890053E-02 at 110iterations 8.8167959E-04 3.1037331E-02 at 120iterations finished qdiffx linear iterations at : 13:56:31 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 8.8167959E-04 3.1037331E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 13:56:32 9.591u 0.239s 0:10.27 95.6% 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 Mon Oct 10 2011 at 13:56:32 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2335 !!! WARNING: HIT 84 has a net charge of 0.5140 !!! WARNING: GLM 85 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.860765 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): -27.16800 25.59700 ymin,ymax (A): 7.763000 48.70100 zmin,zma (A): -13.09600 42.90300 x,y,z range (A): 52.76500 40.93800 55.99900 scale (grids/A): 2.860765 object centre (A): -0.7854996 28.23200 14.90350 number of atom coordinates read : 2335 total number of charged atoms : 2197 net assigned charge : 7.920017 assigned positive charge : 341.1985 centred at (gu) : 94.62278 94.40170 94.84050 assigned negative charge : -333.2791 centred at (gu) : 94.24031 94.01208 94.77025 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 156576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22215 grid for indexing accessible points = 1.400000 m= 75071 mr = 109064 m= 26233 mr = 59159 m= 5977 mr = 19876 m= 836 mr = 4122 m= 52 mr = 435 m= 0 mr = 15 time to grow re-entrant surface = 0.9300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 72074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 17574 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) : 1.907177 object centre at (A) : -0.7854996 28.23200 14.90350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.7523711 0.3419646 midg,1,midg; midg,igrid,midg -4.0163878E-02 0.2504713 1,midg,midg; igrid,midg,midg 0.3870424 0.4456280 gauss-seidel spectral radius is 0.9992613 estimated iterations to convergence 290 setup time was (sec) 1.970000 now iterating at: 13:56:34 rms-change max change #iterations 9.434185 347.9723 at 10iterations 5.550576 156.6469 at 20iterations 3.250170 75.69380 at 30iterations 1.890131 42.34883 at 40iterations 1.096794 22.46771 at 50iterations 0.6360991 13.63125 at 60iterations 0.3687380 8.235617 at 70iterations 0.2126924 3.877988 at 80iterations 0.1225859 2.576538 at 90iterations 7.0900679E-02 1.438940 at 100iterations 4.0813841E-02 0.7778158 at 110iterations 2.3476917E-02 0.4345832 at 120iterations 1.3551696E-02 0.2551956 at 130iterations 7.7863201E-03 0.1560173 at 140iterations 4.4890344E-03 8.6254120E-02 at 150iterations 2.5847275E-03 5.1353455E-02 at 160iterations 1.4915117E-03 2.8202057E-02 at 170iterations 8.6287956E-04 1.7440796E-02 at 180iterations finished qdiffx linear iterations at : 13:56:47 total time elapsed so far: 15.40000 # loops : 180 mean,max change (kT/e) : 8.6287956E-04 1.7440796E-02 energy calculations done at 15.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.62000 DelPhi exited at 13:56:48 15.623u 0.262s 0:16.20 98.0% 0+0k 0+0io 0pf+0w