Sun Oct 9 13:51:37 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 13:51:37 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2451 !!! WARNING: GLM 182 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7031265 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): -1.583000 46.50200 ymin,ymax (A): 36.81400 86.42800 zmin,zma (A): -25.34700 25.28400 x,y,z range (A): 48.08500 49.61400 50.63100 scale (grids/A): 0.7031265 object centre (A): 22.45950 61.62100 -3.1499863E-02 number of atom coordinates read : 2451 total number of charged atoms : 2305 net assigned charge : 5.406020 assigned positive charge : 377.5700 centred at (gu) : 90.12551 89.68842 91.50597 assigned negative charge : -372.1645 centred at (gu) : 90.21259 89.83150 91.51376 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8288 nv = 96 ne = 84 npr = 49067 no. pairs analyzed = 49067 no. exposed pairs = 3085 no. arc points = 21900 no. surface atoms = 1033 nbur = 1418 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 519 mr = 4608 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 4124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2078 ## 189 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9195 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4025540E-08 4.9014833E-08 midg,1,midg; midg,igrid,midg 1.2374966E-07 -3.4173663E-08 1,midg,midg; igrid,midg,midg 8.5039851E-08 -6.1267906E-09 gauss-seidel spectral radius is 0.9894977 estimated iterations to convergence 79 setup time was (sec) 0.3800000 now iterating at: 13:51:37 rms-change max change #iterations 0.2163760 29.39127 at 10iterations 2.7079955E-02 3.292067 at 20iterations 3.8161352E-03 0.5082569 at 30iterations 8.0850668E-04 0.1335831 at 40iterations 2.4014591E-04 3.8002014E-02 at 50iterations finished qdiffx linear iterations at : 13:51:40 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.4014591E-04 3.8002014E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 13:51:41 3.393u 0.189s 0:03.85 92.7% 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 13:51:41 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2451 !!! WARNING: GLM 182 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.109380 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): -1.583000 46.50200 ymin,ymax (A): 36.81400 86.42800 zmin,zma (A): -25.34700 25.28400 x,y,z range (A): 48.08500 49.61400 50.63100 scale (grids/A): 2.109380 object centre (A): 22.45950 61.62100 -3.1499863E-02 number of atom coordinates read : 2451 total number of charged atoms : 2305 net assigned charge : 5.406020 assigned positive charge : 377.5700 centred at (gu) : 90.37590 89.06483 94.51758 assigned negative charge : -372.1645 centred at (gu) : 90.63747 89.49445 94.54091 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 87739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21900 grid for indexing accessible points = 1.400000 m= 33473 mr = 61080 m= 5981 mr = 24899 m= 494 mr = 3724 m= 6 mr = 237 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 37753 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 18296 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) : 0.7031265 object centre at (A) : 22.45950 61.62100 -3.1499863E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9639107E-02 3.5307892E-02 midg,1,midg; midg,igrid,midg 0.1058982 -7.0781242E-03 1,midg,midg; igrid,midg,midg 3.2343199E-03 5.4738633E-03 gauss-seidel spectral radius is 0.9988636 estimated iterations to convergence 235 setup time was (sec) 0.6400000 now iterating at: 13:51:42 rms-change max change #iterations 5.093967 281.3437 at 10iterations 2.542156 96.82764 at 20iterations 1.266914 37.30566 at 30iterations 0.6321064 17.05391 at 40iterations 0.3178384 9.325169 at 50iterations 0.1590837 5.039050 at 60iterations 7.9898857E-02 2.196112 at 70iterations 4.0072188E-02 1.114552 at 80iterations 2.0322556E-02 0.5566158 at 90iterations 1.0290039E-02 0.3101082 at 100iterations 5.3254459E-03 0.1612549 at 110iterations 2.8146342E-03 8.8630676E-02 at 120iterations finished qdiffx linear iterations at : 13:51:49 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.8146342E-03 8.8630676E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 13:51:49 7.942u 0.214s 0:08.51 95.7% 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 13:51:49 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2451 !!! WARNING: GLM 182 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.164069 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): -1.583000 46.50200 ymin,ymax (A): 36.81400 86.42800 zmin,zma (A): -25.34700 25.28400 x,y,z range (A): 48.08500 49.61400 50.63100 scale (grids/A): 3.164069 object centre (A): 22.45950 61.62100 -3.1499863E-02 number of atom coordinates read : 2451 total number of charged atoms : 2305 net assigned charge : 5.406020 assigned positive charge : 377.5700 centred at (gu) : 90.56380 88.59703 96.77627 assigned negative charge : -372.1645 centred at (gu) : 90.95620 89.24155 96.81132 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 202351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21900 grid for indexing accessible points = 1.400000 m= 106107 mr = 147645 m= 40840 mr = 87174 m= 11015 mr = 32870 m= 2087 mr = 8227 m= 242 mr = 1459 m= 6 mr = 157 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.320000 number of dielectric boundary points 85116 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 18440 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) : 2.109380 object centre at (A) : 22.45950 61.62100 -3.1499863E-02 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5685409 0.5897962 midg,1,midg; midg,igrid,midg 1.372925 -7.6237731E-02 1,midg,midg; igrid,midg,midg -1.9652922E-02 2.9999372E-02 gauss-seidel spectral radius is 0.9993120 estimated iterations to convergence 301 setup time was (sec) 1.570000 now iterating at: 13:51:51 rms-change max change #iterations 11.41557 488.6372 at 10iterations 6.788664 159.3303 at 20iterations 4.029961 73.73073 at 30iterations 2.388324 42.24791 at 40iterations 1.414205 25.19555 at 50iterations 0.8342315 15.85497 at 60iterations 0.4935290 7.842903 at 70iterations 0.2911932 5.061838 at 80iterations 0.1715840 3.401958 at 90iterations 0.1011979 1.707376 at 100iterations 5.9809387E-02 1.004713 at 110iterations 3.5494909E-02 0.5594673 at 120iterations 2.1310261E-02 0.4044495 at 130iterations 1.2983819E-02 0.2236786 at 140iterations 8.1562139E-03 0.1434097 at 150iterations 5.3539826E-03 0.1022377 at 160iterations 3.7178698E-03 7.3955536E-02 at 170iterations 2.7458861E-03 6.0935974E-02 at 180iterations finished qdiffx linear iterations at : 13:52:03 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 2.7458861E-03 6.0935974E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.28000 DelPhi exited at 13:52:03 13.279u 0.217s 0:13.76 97.9% 0+0k 0+0io 0pf+0w