Mon Oct 10 17:01:56 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 17:01:56 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4303 !!! WARNING: GLM 169 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5538356 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): -15.61500 36.63200 ymin,ymax (A): -31.96000 32.31900 zmin,zma (A): -4.195000 58.05700 x,y,z range (A): 52.24700 64.27900 62.25200 scale (grids/A): 0.5538356 object centre (A): 10.50850 0.1794996 26.93100 number of atom coordinates read : 4303 total number of charged atoms : 4139 net assigned charge : 0.4060281 assigned positive charge : 648.5430 centred at (gu) : 90.15060 90.72622 89.36372 assigned negative charge : -648.1412 centred at (gu) : 90.01929 90.80226 89.44329 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8559 nv = 96 ne = 84 npr = 86658 no. pairs analyzed = 86658 no. exposed pairs = 5635 no. arc points = 38814 no. surface atoms = 1891 nbur = 2412 mkacc time = 0.2100000 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 = 1.568000 m= 386 mr = 4441 m= 1 mr = 25 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 0.4800000 number of dielectric boundary points 4480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3992 ## 519 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 11330 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2342966E-09 -8.5918028E-10 midg,1,midg; midg,igrid,midg 8.4291180E-10 -1.1508001E-09 1,midg,midg; igrid,midg,midg -1.6311930E-09 1.7706293E-09 gauss-seidel spectral radius is 0.9832909 estimated iterations to convergence 64 setup time was (sec) 0.7500000 now iterating at: 17:01:57 rms-change max change #iterations 9.3996361E-02 12.46450 at 10iterations 6.7181764E-03 0.8110619 at 20iterations 5.1225978E-04 7.5820923E-02 at 30iterations 5.6750629E-05 9.3984604E-03 at 40iterations 1.0437617E-05 1.8529892E-03 at 50iterations finished qdiffx linear iterations at : 17:02:00 total time elapsed so far: 4.140000 # loops : 50 mean,max change (kT/e) : 1.0437617E-05 1.8529892E-03 energy calculations done at 4.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 17:02:01 4.320u 0.242s 0:05.28 86.3% 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 17:02:01 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4303 !!! WARNING: GLM 169 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.661507 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): -15.61500 36.63200 ymin,ymax (A): -31.96000 32.31900 zmin,zma (A): -4.195000 58.05700 x,y,z range (A): 52.24700 64.27900 62.25200 scale (grids/A): 1.661507 object centre (A): 10.50850 0.1794996 26.93100 number of atom coordinates read : 4303 total number of charged atoms : 4139 net assigned charge : 0.4060281 assigned positive charge : 648.5430 centred at (gu) : 90.45049 92.17735 88.08949 assigned negative charge : -648.1412 centred at (gu) : 90.05764 92.40629 88.32956 start vw surface at 0.2200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 94992 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38814 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30158 mr = 65000 m= 3501 mr = 20439 m= 134 mr = 1637 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 151 time to turn everything in is 0.8300000 number of dielectric boundary points 41694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 426 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 31833 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) : 0.5538356 object centre at (A) : 10.50850 0.1794996 26.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4943253E-03 -8.4425518E-03 midg,1,midg; midg,igrid,midg -7.4927732E-03 -2.3310514E-02 1,midg,midg; igrid,midg,midg -9.4264131E-03 1.8086150E-02 gauss-seidel spectral radius is 0.9983918 estimated iterations to convergence 198 setup time was (sec) 1.180000 now iterating at: 17:02:03 rms-change max change #iterations 4.296600 154.5212 at 10iterations 1.884832 58.41032 at 20iterations 0.8254783 27.44959 at 30iterations 0.3631754 11.25549 at 40iterations 0.1591804 5.015190 at 50iterations 6.9962680E-02 2.106216 at 60iterations 3.0703904E-02 0.9457006 at 70iterations 1.3484372E-02 0.4031850 at 80iterations 5.9500318E-03 0.1864686 at 90iterations 2.6286119E-03 8.8367462E-02 at 100iterations 1.1632828E-03 3.5525084E-02 at 110iterations 5.2379386E-04 1.5998840E-02 at 120iterations finished qdiffx linear iterations at : 17:02:11 total time elapsed so far: 9.710000 # loops : 120 mean,max change (kT/e) : 5.2379386E-04 1.5998840E-02 energy calculations done at 9.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.890000 DelPhi exited at 17:02:12 9.896u 0.282s 0:11.28 90.1% 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 17:02:12 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4303 !!! WARNING: GLM 169 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.492260 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): -15.61500 36.63200 ymin,ymax (A): -31.96000 32.31900 zmin,zma (A): -4.195000 58.05700 x,y,z range (A): 52.24700 64.27900 62.25200 scale (grids/A): 2.492260 object centre (A): 10.50850 0.1794996 26.93100 number of atom coordinates read : 4303 total number of charged atoms : 4139 net assigned charge : 0.4060281 assigned positive charge : 648.5430 centred at (gu) : 90.67548 93.26576 87.13392 assigned negative charge : -648.1412 centred at (gu) : 90.08633 93.60937 87.49432 start vw surface at 0.1700000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 221007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38814 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 103896 mr = 159642 m= 30462 mr = 81460 m= 5478 mr = 22378 m= 471 mr = 3454 m= 9 mr = 240 m= 0 mr = 0 time to grow re-entrant surface = 1.060000 no. cavity mid-points inaccessible to solvent = 501 time to turn everything in is 1.780000 number of dielectric boundary points 94149 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.940000 number of grid points assigned charge 33091 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) : 1.661507 object centre at (A) : 10.50850 0.1794996 26.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1187675 -8.5096553E-02 midg,1,midg; midg,igrid,midg -0.4189013 -0.4823964 1,midg,midg; igrid,midg,midg -0.1302879 0.2605328 gauss-seidel spectral radius is 0.9992412 estimated iterations to convergence 287 setup time was (sec) 2.150000 now iterating at: 17:02:15 rms-change max change #iterations 11.04659 365.8916 at 10iterations 6.522573 132.0846 at 20iterations 3.825990 81.73416 at 30iterations 2.234149 45.47046 at 40iterations 1.297782 27.31943 at 50iterations 0.7515803 15.42311 at 60iterations 0.4343685 9.582174 at 70iterations 0.2503113 5.248100 at 80iterations 0.1439689 2.868467 at 90iterations 8.2722917E-02 1.653061 at 100iterations 4.7646344E-02 0.8570614 at 110iterations 2.7251486E-02 0.4805179 at 120iterations 1.5622701E-02 0.3410634 at 130iterations 8.9239925E-03 0.1527748 at 140iterations 5.1258150E-03 9.1365874E-02 at 150iterations 2.9310647E-03 5.8968067E-02 at 160iterations 1.6779610E-03 3.3087254E-02 at 170iterations 9.5891103E-04 1.5863419E-02 at 180iterations finished qdiffx linear iterations at : 17:02:29 total time elapsed so far: 16.62000 # loops : 180 mean,max change (kT/e) : 9.5891103E-04 1.5863419E-02 energy calculations done at 16.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.82000 DelPhi exited at 17:02:30 16.822u 0.338s 0:18.07 94.9% 0+0k 0+0io 0pf+0w