Sat Oct 15 14:34:06 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+sph.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 = amb.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 Sat Oct 15 2011 at 14:34:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2867 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6207714 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): -8.659000 48.68900 ymin,ymax (A): -8.163000 38.83500 zmin,zma (A): -0.4890000 54.92500 x,y,z range (A): 57.34800 46.99800 55.41400 scale (grids/A): 0.6207714 object centre (A): 20.01500 15.33600 27.21800 number of atom coordinates read : 2867 total number of charged atoms : 2726 net assigned charge : -2.499973 assigned positive charge : 429.6701 centred at (gu) : 89.11985 89.65488 89.18375 assigned negative charge : -432.1712 centred at (gu) : 89.03711 89.58613 89.16361 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7517 nv = 96 ne = 84 npr = 57010 no. pairs analyzed = 57010 no. exposed pairs = 3783 no. arc points = 26454 no. surface atoms = 1274 nbur = 1593 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 3979 m= 2 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.2100000 number of dielectric boundary points 3884 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2648 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9118 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1628647E-09 -3.8261988E-10 midg,1,midg; midg,igrid,midg -7.7660314E-09 2.9531555E-09 1,midg,midg; igrid,midg,midg -1.0061100E-08 3.4657321E-09 gauss-seidel spectral radius is 0.9865925 estimated iterations to convergence 71 setup time was (sec) 0.4300000 now iterating at: 14:34:07 rms-change max change #iterations 0.1298806 16.69382 at 10iterations 1.1999676E-02 1.767345 at 20iterations 1.1144705E-03 0.1655717 at 30iterations 1.0182228E-04 1.4107943E-02 at 40iterations 9.5369369E-06 1.4572144E-03 at 50iterations finished qdiffx linear iterations at : 14:34:12 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 9.5369369E-06 1.4572144E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 14:34:13 3.708u 0.238s 0:06.70 58.6% 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 Sat Oct 15 2011 at 14:34:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2867 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.862314 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): -8.659000 48.68900 ymin,ymax (A): -8.163000 38.83500 zmin,zma (A): -0.4890000 54.92500 x,y,z range (A): 57.34800 46.99800 55.41400 scale (grids/A): 1.862314 object centre (A): 20.01500 15.33600 27.21800 number of atom coordinates read : 2867 total number of charged atoms : 2726 net assigned charge : -2.499973 assigned positive charge : 429.6701 centred at (gu) : 87.35857 88.96352 87.55035 assigned negative charge : -432.1712 centred at (gu) : 87.11106 88.75829 87.49047 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81278 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26454 grid for indexing accessible points = 1.400000 m= 27696 mr = 55328 m= 3806 mr = 19666 m= 175 mr = 2081 m= 5 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1468 time to turn everything in is 0.4200000 number of dielectric boundary points 35846 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 230 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 21404 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) : 0.6207714 object centre at (A) : 20.01500 15.33600 27.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0974771E-02 5.3192773E-03 midg,1,midg; midg,igrid,midg -2.3952406E-02 -3.9076473E-04 1,midg,midg; igrid,midg,midg -4.8257805E-02 2.5348490E-02 gauss-seidel spectral radius is 0.9986078 estimated iterations to convergence 212 setup time was (sec) 0.6500000 now iterating at: 14:34:14 rms-change max change #iterations 4.267942 167.1265 at 10iterations 1.976525 75.94293 at 20iterations 0.9191775 33.73421 at 30iterations 0.4261386 12.67222 at 40iterations 0.1975750 5.929229 at 50iterations 9.1668464E-02 2.852894 at 60iterations 4.2604651E-02 1.463474 at 70iterations 1.9781932E-02 0.6550674 at 80iterations 9.1916192E-03 0.2816007 at 90iterations 4.2857463E-03 0.1450682 at 100iterations 1.9866016E-03 6.1176300E-02 at 110iterations 9.2514412E-04 2.9973984E-02 at 120iterations finished qdiffx linear iterations at : 14:34:28 total time elapsed so far: 8.310000 # loops : 120 mean,max change (kT/e) : 9.2514412E-04 2.9973984E-02 energy calculations done at 8.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.440000 DelPhi exited at 14:34:28 8.446u 0.230s 0:15.56 55.7% 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 Sat Oct 15 2011 at 14:34:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2867 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.793471 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): -8.659000 48.68900 ymin,ymax (A): -8.163000 38.83500 zmin,zma (A): -0.4890000 54.92500 x,y,z range (A): 57.34800 46.99800 55.41400 scale (grids/A): 2.793471 object centre (A): 20.01500 15.33600 27.21800 number of atom coordinates read : 2867 total number of charged atoms : 2726 net assigned charge : -2.499973 assigned positive charge : 429.6701 centred at (gu) : 86.03763 88.44522 86.32540 assigned negative charge : -432.1712 centred at (gu) : 85.66646 88.13729 86.23550 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 188380 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26454 grid for indexing accessible points = 1.400000 m= 91275 mr = 134709 m= 30555 mr = 73243 m= 6361 mr = 23669 m= 691 mr = 4406 m= 39 mr = 402 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 5359 time to turn everything in is 1.040000 number of dielectric boundary points 80860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.150000 number of grid points assigned charge 21806 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) : 1.862314 object centre at (A) : 20.01500 15.33600 27.21800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1718540 -0.2216531 midg,1,midg; midg,igrid,midg -0.2339723 -1.7045934E-02 1,midg,midg; igrid,midg,midg -0.6112173 0.3974489 gauss-seidel spectral radius is 0.9992698 estimated iterations to convergence 292 setup time was (sec) 1.320000 now iterating at: 14:34:30 rms-change max change #iterations 10.39245 280.2098 at 10iterations 6.178537 227.6051 at 20iterations 3.625401 88.89177 at 30iterations 2.126922 49.60219 at 40iterations 1.238154 25.80051 at 50iterations 0.7204479 13.84113 at 60iterations 0.4178112 8.025959 at 70iterations 0.2434056 4.737780 at 80iterations 0.1406226 2.769751 at 90iterations 8.1569940E-02 1.512384 at 100iterations 4.7123563E-02 0.8490314 at 110iterations 2.7285896E-02 0.5013762 at 120iterations 1.5741685E-02 0.2961578 at 130iterations 9.0847490E-03 0.1691513 at 140iterations 5.2443733E-03 9.6820951E-02 at 150iterations 3.0316445E-03 5.1715851E-02 at 160iterations 1.7496715E-03 2.8667450E-02 at 170iterations 1.0129587E-03 1.8293858E-02 at 180iterations finished qdiffx linear iterations at : 14:34:55 total time elapsed so far: 14.26000 # loops : 180 mean,max change (kT/e) : 1.0129587E-03 1.8293858E-02 energy calculations done at 14.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.39000 DelPhi exited at 14:34:55 14.387u 0.290s 0:26.96 54.4% 0+0k 0+0io 0pf+0w