Tue Oct 11 08:34:31 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 Tue Oct 11 2011 at 08:34:31 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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: 0.7307811 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): 25.60800 72.02600 ymin,ymax (A): -18.75400 29.96100 zmin,zma (A): 3.919000 46.33800 x,y,z range (A): 46.41800 48.71500 42.41900 scale (grids/A): 0.7307811 object centre (A): 48.81700 5.603500 25.12850 number of atom coordinates read : 2281 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 318.3760 centred at (gu) : 89.10233 90.55315 90.29821 assigned negative charge : -312.4312 centred at (gu) : 89.23532 90.48791 90.38197 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7730 nv = 96 ne = 84 npr = 41574 no. pairs analyzed = 41574 no. exposed pairs = 2536 no. arc points = 17336 no. surface atoms = 863 nbur = 1418 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 554 mr = 4554 m= 4 mr = 117 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 0.2800000 number of dielectric boundary points 3617 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1528 ## 133 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8198 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4426246E-07 1.5866251E-08 midg,1,midg; midg,igrid,midg 2.8058020E-08 1.5261627E-07 1,midg,midg; igrid,midg,midg 2.2772687E-07 -2.1022744E-08 gauss-seidel spectral radius is 0.9902350 estimated iterations to convergence 82 setup time was (sec) 0.5100000 now iterating at: 08:34:32 rms-change max change #iterations 0.2298981 29.04915 at 10iterations 3.0907674E-02 4.286362 at 20iterations 4.3529333E-03 0.5799255 at 30iterations 7.5648195E-04 0.1003857 at 40iterations 2.0001449E-04 2.2985458E-02 at 50iterations finished qdiffx linear iterations at : 08:34:35 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 2.0001449E-04 2.2985458E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 08:34:35 3.375u 0.211s 0:04.05 88.3% 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 Tue Oct 11 2011 at 08:34:35 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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: 2.192343 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): 25.60800 72.02600 ymin,ymax (A): -18.75400 29.96100 zmin,zma (A): 3.919000 46.33800 x,y,z range (A): 46.41800 48.71500 42.41900 scale (grids/A): 2.192343 object centre (A): 48.81700 5.603500 25.12850 number of atom coordinates read : 2281 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 318.3760 centred at (gu) : 87.30698 91.65929 90.89446 assigned negative charge : -312.4312 centred at (gu) : 87.70612 91.46371 91.14600 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81339 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17336 grid for indexing accessible points = 1.400000 m= 34388 mr = 58457 m= 7196 mr = 26540 m= 742 mr = 5006 m= 30 mr = 411 m= 0 mr = 6 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 33275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 15537 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) : 0.7307811 object centre at (A) : 48.81700 5.603500 25.12850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4721256E-02 3.0520873E-02 midg,1,midg; midg,igrid,midg 4.3334585E-02 3.3339120E-02 1,midg,midg; igrid,midg,midg 4.7734261E-02 -5.6314528E-02 gauss-seidel spectral radius is 0.9988965 estimated iterations to convergence 238 setup time was (sec) 0.9300000 now iterating at: 08:34:37 rms-change max change #iterations 4.928426 200.4855 at 10iterations 2.485501 82.78439 at 20iterations 1.261145 39.24915 at 30iterations 0.6371606 17.48456 at 40iterations 0.3218617 8.911748 at 50iterations 0.1636740 5.150791 at 60iterations 8.3080798E-02 2.253746 at 70iterations 4.2231914E-02 1.199944 at 80iterations 2.1488793E-02 0.6774826 at 90iterations 1.1065583E-02 0.3411360 at 100iterations 5.6976131E-03 0.1577797 at 110iterations 3.0094180E-03 8.9389801E-02 at 120iterations finished qdiffx linear iterations at : 08:34:43 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 3.0094180E-03 8.9389801E-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) 7.990000 DelPhi exited at 08:34:44 7.996u 0.225s 0:08.55 96.0% 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 Tue Oct 11 2011 at 08:34:44 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2281 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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: 3.288515 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): 25.60800 72.02600 ymin,ymax (A): -18.75400 29.96100 zmin,zma (A): 3.919000 46.33800 x,y,z range (A): 46.41800 48.71500 42.41900 scale (grids/A): 3.288515 object centre (A): 48.81700 5.603500 25.12850 number of atom coordinates read : 2281 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 318.3760 centred at (gu) : 85.96043 92.48904 91.34174 assigned negative charge : -312.4312 centred at (gu) : 86.55927 92.19559 91.71906 start vw surface at 0.1600000 fill in re-entrant regions at 0.9100000 boundary points on vw surface= 187083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17336 grid for indexing accessible points = 1.400000 m= 105275 mr = 139989 m= 45312 mr = 88561 m= 13820 mr = 37863 m= 3039 mr = 10939 m= 408 mr = 2241 m= 34 mr = 279 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.070000 number of dielectric boundary points 75075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 15640 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) : 2.192343 object centre at (A) : 48.81700 5.603500 25.12850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1122725 0.2538905 midg,1,midg; midg,igrid,midg 0.2934214 0.1712791 1,midg,midg; igrid,midg,midg 0.4722559 -0.6527253 gauss-seidel spectral radius is 0.9993131 estimated iterations to convergence 301 setup time was (sec) 2.400000 now iterating at: 08:34:47 rms-change max change #iterations 10.73069 358.2946 at 10iterations 6.384366 128.9722 at 20iterations 3.788670 78.74992 at 30iterations 2.253271 53.33508 at 40iterations 1.333776 23.87492 at 50iterations 0.7876505 13.56358 at 60iterations 0.4653434 8.582013 at 70iterations 0.2754612 5.441339 at 80iterations 0.1624439 2.763244 at 90iterations 9.5937319E-02 1.635990 at 100iterations 5.6718905E-02 1.004624 at 110iterations 3.3647012E-02 0.5649033 at 120iterations 2.0210672E-02 0.3451443 at 130iterations 1.2289260E-02 0.2290039 at 140iterations 7.6839454E-03 0.1535435 at 150iterations 4.9827090E-03 0.1015701 at 160iterations 3.4074164E-03 6.2534332E-02 at 170iterations 2.4764487E-03 4.5356750E-02 at 180iterations finished qdiffx linear iterations at : 08:34:57 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 2.4764487E-03 4.5356750E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 08:34:58 13.049u 0.212s 0:13.64 97.1% 0+0k 0+0io 0pf+0w