Sun Oct 9 15:20:57 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 15:20:58 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5659 !!! WARNING: HIR 555 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.4995930 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): 67.47900 138.7370 ymin,ymax (A): -6.196000 57.03800 zmin,zma (A): -3.243000 65.75700 x,y,z range (A): 71.25800 63.23400 69.00000 scale (grids/A): 0.4995930 object centre (A): 103.1080 25.42100 31.25700 number of atom coordinates read : 5659 total number of charged atoms : 5488 net assigned charge : -4.485955 assigned positive charge : 867.0055 centred at (gu) : 89.69753 90.83643 90.18052 assigned negative charge : -871.4990 centred at (gu) : 89.76873 90.77151 90.29230 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8557 nv = 96 ne = 84 npr = 117550 no. pairs analyzed = 117550 no. exposed pairs = 6363 no. arc points = 43946 no. surface atoms = 2146 nbur = 3513 mkacc time = 0.2000000 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 = 1.708000 m= 269 mr = 4679 m= 0 mr = 6 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.3700000 number of dielectric boundary points 4141 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4253 ## 628 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 11735 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6737345E-10 -2.7492278E-10 midg,1,midg; midg,igrid,midg -1.3395561E-10 1.0908251E-10 1,midg,midg; igrid,midg,midg 1.0706740E-10 -1.6616940E-10 gauss-seidel spectral radius is 0.9795614 estimated iterations to convergence 58 setup time was (sec) 0.5500000 now iterating at: 15:20:58 rms-change max change #iterations 6.6633224E-02 9.830944 at 10iterations 3.9857533E-03 0.5967627 at 20iterations 4.7254481E-04 5.8640480E-02 at 30iterations 1.2120626E-04 1.4164925E-02 at 40iterations 3.7848757E-05 4.3360591E-03 at 50iterations finished qdiffx linear iterations at : 15:21:01 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 3.7848757E-05 4.3360591E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 15:21:02 3.596u 0.175s 0:04.05 92.8% 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 15:21:02 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5659 !!! WARNING: HIR 555 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.498779 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): 67.47900 138.7370 ymin,ymax (A): -6.196000 57.03800 zmin,zma (A): -3.243000 65.75700 x,y,z range (A): 71.25800 63.23400 69.00000 scale (grids/A): 1.498779 object centre (A): 103.1080 25.42100 31.25700 number of atom coordinates read : 5659 total number of charged atoms : 5488 net assigned charge : -4.485955 assigned positive charge : 867.0055 centred at (gu) : 89.09097 92.50743 90.53979 assigned negative charge : -871.4990 centred at (gu) : 89.30644 92.31472 90.87686 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 98620 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43946 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 27700 mr = 70103 m= 2213 mr = 18880 m= 33 mr = 894 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 3933 time to turn everything in is 0.4600000 number of dielectric boundary points 38689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 626 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 40887 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) : 0.4995930 object centre at (A) : 103.1080 25.42100 31.25700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7923569E-03 -1.6359775E-03 midg,1,midg; midg,igrid,midg -1.0185431E-02 5.3973417E-03 1,midg,midg; igrid,midg,midg -1.8846383E-02 -8.8757202E-03 gauss-seidel spectral radius is 0.9980797 estimated iterations to convergence 181 setup time was (sec) 0.6700000 now iterating at: 15:21:03 rms-change max change #iterations 4.031747 140.5464 at 10iterations 1.640462 52.84535 at 20iterations 0.6680462 20.38330 at 30iterations 0.2726552 8.177444 at 40iterations 0.1109513 3.639784 at 50iterations 4.5357265E-02 1.425348 at 60iterations 1.8564899E-02 0.5692177 at 70iterations 7.5849537E-03 0.2207718 at 80iterations 3.1167220E-03 0.1023989 at 90iterations 1.2966130E-03 4.3140411E-02 at 100iterations 5.5436703E-04 1.7799377E-02 at 110iterations 2.5031547E-04 7.9650879E-03 at 120iterations finished qdiffx linear iterations at : 15:21:10 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 2.5031547E-04 7.9650879E-03 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 15:21:10 8.039u 0.218s 0:08.53 96.6% 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 Sun Oct 9 2011 at 15:21:10 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: 286 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5659 !!! WARNING: HIR 555 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.248168 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): 67.47900 138.7370 ymin,ymax (A): -6.196000 57.03800 zmin,zma (A): -3.243000 65.75700 x,y,z range (A): 71.25800 63.23400 69.00000 scale (grids/A): 2.248168 object centre (A): 103.1080 25.42100 31.25700 number of atom coordinates read : 5659 total number of charged atoms : 5488 net assigned charge : -4.485955 assigned positive charge : 867.0055 centred at (gu) : 88.63586 93.76056 90.80941 assigned negative charge : -871.4990 centred at (gu) : 88.95958 93.47215 91.31519 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 230738 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43946 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 101475 mr = 172360 m= 24571 mr = 80473 m= 3104 mr = 17930 m= 129 mr = 1839 m= 0 mr = 20 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 12822 time to turn everything in is 1.160000 number of dielectric boundary points 87395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 43745 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) : 1.498779 object centre at (A) : 103.1080 25.42100 31.25700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8722938E-02 0.1066080 midg,1,midg; midg,igrid,midg -0.2285008 0.1617373 1,midg,midg; igrid,midg,midg -0.5815207 5.9168879E-02 gauss-seidel spectral radius is 0.9991601 estimated iterations to convergence 273 setup time was (sec) 1.410000 now iterating at: 15:21:12 rms-change max change #iterations 10.92476 306.9430 at 10iterations 6.195230 127.5293 at 20iterations 3.496372 72.56074 at 30iterations 1.960686 43.18015 at 40iterations 1.099935 20.59426 at 50iterations 0.6149210 10.97471 at 60iterations 0.3425851 5.917362 at 70iterations 0.1911087 3.854904 at 80iterations 0.1061678 2.056156 at 90iterations 5.9130859E-02 1.056572 at 100iterations 3.2851011E-02 0.5904617 at 110iterations 1.8258432E-02 0.3038788 at 120iterations 1.0128281E-02 0.1712646 at 130iterations 5.6213471E-03 0.1041031 at 140iterations 3.1224668E-03 5.3302765E-02 at 150iterations 1.7370067E-03 2.9954910E-02 at 160iterations 9.6694822E-04 1.7761230E-02 at 170iterations 5.3955900E-04 9.4337463E-03 at 180iterations finished qdiffx linear iterations at : 15:21:23 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 5.3955900E-04 9.4337463E-03 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.13000 DelPhi exited at 15:21:24 13.131u 0.211s 0:13.70 97.3% 0+0k 0+0io 0pf+0w