Tue Oct 11 08:22:40 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 08:22:40 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3111 !!! WARNING: GLM 341 has a net charge of -0.0940 !!! WARNING: HIR 383 has a net charge of 0.5140 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: 0.5771164 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): 96.06800 150.2160 ymin,ymax (A): -14.68900 42.07200 zmin,zma (A): 5.517000 67.20300 x,y,z range (A): 54.14799 56.76100 61.68600 scale (grids/A): 0.5771164 object centre (A): 123.1420 13.69150 36.36000 number of atom coordinates read : 3111 total number of charged atoms : 2969 net assigned charge : -6.079976 assigned positive charge : 465.7569 centred at (gu) : 90.99673 89.34043 89.96667 assigned negative charge : -471.8380 centred at (gu) : 90.97417 89.31252 90.01329 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6757 nv = 96 ne = 84 npr = 63874 no. pairs analyzed = 63874 no. exposed pairs = 3959 no. arc points = 27291 no. surface atoms = 1331 nbur = 1780 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 316 mr = 3577 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2849 ## 313 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8725 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1917250E-10 -2.1782274E-09 midg,1,midg; midg,igrid,midg -2.0926441E-09 -5.2993604E-10 1,midg,midg; igrid,midg,midg -1.3365888E-09 -9.0259666E-10 gauss-seidel spectral radius is 0.9845146 estimated iterations to convergence 66 setup time was (sec) 0.6700000 now iterating at: 08:22:41 rms-change max change #iterations 0.1018391 16.02509 at 10iterations 8.0032563E-03 1.162421 at 20iterations 9.8297349E-04 0.1495991 at 30iterations 2.7473425E-04 4.1090965E-02 at 40iterations 9.4043156E-05 1.4243126E-02 at 50iterations finished qdiffx linear iterations at : 08:22:45 total time elapsed so far: 4.860000 # loops : 50 mean,max change (kT/e) : 9.4043156E-05 1.4243126E-02 energy calculations done at 4.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.040000 DelPhi exited at 08:22:46 5.047u 0.414s 0:05.78 94.2% 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 Tue Oct 11 2011 at 08:22:46 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3111 !!! WARNING: GLM 341 has a net charge of -0.0940 !!! WARNING: HIR 383 has a net charge of 0.5140 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: 1.731349 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): 96.06800 150.2160 ymin,ymax (A): -14.68900 42.07200 zmin,zma (A): 5.517000 67.20300 x,y,z range (A): 54.14799 56.76100 61.68600 scale (grids/A): 1.731349 object centre (A): 123.1420 13.69150 36.36000 number of atom coordinates read : 3111 total number of charged atoms : 2969 net assigned charge : -6.079976 assigned positive charge : 465.7569 centred at (gu) : 92.98976 88.02074 89.89914 assigned negative charge : -471.8380 centred at (gu) : 92.92214 87.93726 90.03991 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74117 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27291 grid for indexing accessible points = 1.400000 m= 25082 mr = 50658 m= 3223 mr = 17700 m= 114 mr = 1743 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1323 time to turn everything in is 0.6400000 number of dielectric boundary points 32418 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 286 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 23029 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) : 0.5771164 object centre at (A) : 123.1420 13.69150 36.36000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5706228E-02 -3.3573989E-02 midg,1,midg; midg,igrid,midg -8.2961833E-03 3.3520591E-03 1,midg,midg; igrid,midg,midg -9.2128674E-03 2.6594978E-03 gauss-seidel spectral radius is 0.9984062 estimated iterations to convergence 199 setup time was (sec) 0.9900000 now iterating at: 08:22:47 rms-change max change #iterations 3.916021 179.0596 at 10iterations 1.721318 62.37835 at 20iterations 0.7549827 25.28166 at 30iterations 0.3336382 11.98346 at 40iterations 0.1468967 4.597020 at 50iterations 6.4898998E-02 2.500216 at 60iterations 2.8612483E-02 0.9604492 at 70iterations 1.2679536E-02 0.4082508 at 80iterations 5.6793434E-03 0.1826172 at 90iterations 2.6172439E-03 9.0613365E-02 at 100iterations 1.2667163E-03 5.6087494E-02 at 110iterations 6.5879273E-04 2.3914337E-02 at 120iterations finished qdiffx linear iterations at : 08:22:58 total time elapsed so far: 11.80000 # loops : 120 mean,max change (kT/e) : 6.5879273E-04 2.3914337E-02 energy calculations done at 11.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 08:22:59 11.972u 0.491s 0:12.93 96.3% 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 08:22:59 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: 336 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3111 !!! WARNING: GLM 341 has a net charge of -0.0940 !!! WARNING: HIR 383 has a net charge of 0.5140 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: 2.597024 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): 96.06800 150.2160 ymin,ymax (A): -14.68900 42.07200 zmin,zma (A): 5.517000 67.20300 x,y,z range (A): 54.14799 56.76100 61.68600 scale (grids/A): 2.597024 object centre (A): 123.1420 13.69150 36.36000 number of atom coordinates read : 3111 total number of charged atoms : 2969 net assigned charge : -6.079976 assigned positive charge : 465.7569 centred at (gu) : 94.48434 87.03081 89.84829 assigned negative charge : -471.8380 centred at (gu) : 94.38301 86.90569 90.05962 start vw surface at 0.1300000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 171447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27291 grid for indexing accessible points = 1.400000 m= 83606 mr = 123298 m= 27256 mr = 66904 m= 5392 mr = 21008 m= 503 mr = 3727 m= 7 mr = 243 m= 0 mr = 2 time to grow re-entrant surface = 0.9800001 no. cavity mid-points inaccessible to solvent = 4770 time to turn everything in is 1.610000 number of dielectric boundary points 73029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 23741 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) : 1.731349 object centre at (A) : 123.1420 13.69150 36.36000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3435378 -0.3834507 midg,1,midg; midg,igrid,midg 5.9386931E-02 2.5891071E-02 1,midg,midg; igrid,midg,midg -0.1824582 0.1135369 gauss-seidel spectral radius is 0.9992086 estimated iterations to convergence 281 setup time was (sec) 1.990000 now iterating at: 08:23:02 rms-change max change #iterations 9.678865 294.1330 at 10iterations 5.622581 140.4761 at 20iterations 3.221039 69.32953 at 30iterations 1.847157 38.80473 at 40iterations 1.050081 21.70991 at 50iterations 0.5967062 12.29467 at 60iterations 0.3394270 7.062408 at 70iterations 0.1922589 4.119232 at 80iterations 0.1087312 2.106082 at 90iterations 6.1627146E-02 1.316120 at 100iterations 3.4942709E-02 0.7210646 at 110iterations 1.9702774E-02 0.4302521 at 120iterations 1.1214897E-02 0.2216568 at 130iterations 6.3849897E-03 0.1198692 at 140iterations 3.6610435E-03 7.1610451E-02 at 150iterations 2.1341366E-03 4.6686172E-02 at 160iterations 1.2773953E-03 2.5897026E-02 at 170iterations 7.9791644E-04 1.5486717E-02 at 180iterations finished qdiffx linear iterations at : 08:23:20 total time elapsed so far: 20.26000 # loops : 180 mean,max change (kT/e) : 7.9791644E-04 1.5486717E-02 energy calculations done at 20.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.44000 DelPhi exited at 08:23:21 20.442u 0.499s 0:21.37 97.9% 0+0k 0+0io 0pf+0w