Mon Oct 10 17:03:56 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 17:03:56 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4805 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 0.5126950 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): -18.72500 36.71400 ymin,ymax (A): -30.65200 34.29400 zmin,zma (A): -3.969000 65.46800 x,y,z range (A): 55.43900 64.94600 69.43700 scale (grids/A): 0.5126950 object centre (A): 8.994500 1.821001 30.74950 number of atom coordinates read : 4805 total number of charged atoms : 4555 net assigned charge : 9.706057 assigned positive charge : 722.5015 centred at (gu) : 90.23886 90.60728 88.30260 assigned negative charge : -712.7997 centred at (gu) : 90.13858 90.65658 88.26788 start vw surface at 0.2600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 8049 nv = 96 ne = 84 npr = 96337 no. pairs analyzed = 96337 no. exposed pairs = 6162 no. arc points = 42935 no. surface atoms = 2057 nbur = 2748 mkacc time = 0.2300000 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 = 1.652000 m= 272 mr = 4124 m= 4 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 4190 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4090 ## 604 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 10608 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1283383E-11 1.6180353E-10 midg,1,midg; midg,igrid,midg 2.4847227E-10 1.3945599E-11 1,midg,midg; igrid,midg,midg -1.2507026E-10 4.5980281E-10 gauss-seidel spectral radius is 0.9805490 estimated iterations to convergence 59 setup time was (sec) 0.7800000 now iterating at: 17:03:57 rms-change max change #iterations 6.9762237E-02 10.68958 at 10iterations 4.3650605E-03 0.7264404 at 20iterations 6.5448106E-04 9.0610504E-02 at 30iterations 2.5784908E-04 3.8145661E-02 at 40iterations 1.1227221E-04 1.7087102E-02 at 50iterations finished qdiffx linear iterations at : 17:04:00 total time elapsed so far: 3.690000 # loops : 50 mean,max change (kT/e) : 1.1227221E-04 1.7087102E-02 energy calculations done at 3.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.890000 DelPhi exited at 17:04:02 3.889u 0.190s 0:05.49 74.1% 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 17:04:02 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4805 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.538085 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): -18.72500 36.71400 ymin,ymax (A): -30.65200 34.29400 zmin,zma (A): -3.969000 65.46800 x,y,z range (A): 55.43900 64.94600 69.43700 scale (grids/A): 1.538085 object centre (A): 8.994500 1.821001 30.74950 number of atom coordinates read : 4805 total number of charged atoms : 4555 net assigned charge : 9.706057 assigned positive charge : 722.5015 centred at (gu) : 90.71519 91.82072 84.90636 assigned negative charge : -712.7997 centred at (gu) : 90.41563 91.96947 84.80302 start vw surface at 0.2000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 91228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42935 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 26355 mr = 62363 m= 2278 mr = 17358 m= 44 mr = 930 m= 0 mr = 2 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 154 time to turn everything in is 0.6800000 number of dielectric boundary points 39252 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 556 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 34243 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) : 0.5126950 object centre at (A) : 8.994500 1.821001 30.74950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1022413E-03 2.2078149E-02 midg,1,midg; midg,igrid,midg 1.1553993E-02 -8.0873379E-03 1,midg,midg; igrid,midg,midg -2.8222895E-04 1.2305691E-02 gauss-seidel spectral radius is 0.9981368 estimated iterations to convergence 184 setup time was (sec) 1.010000 now iterating at: 17:04:03 rms-change max change #iterations 3.877614 154.2911 at 10iterations 1.597727 55.79033 at 20iterations 0.6601695 22.35846 at 30iterations 0.2729368 10.16517 at 40iterations 0.1121930 3.795508 at 50iterations 4.6622451E-02 1.575237 at 60iterations 1.9257395E-02 0.5582771 at 70iterations 7.9951901E-03 0.2453461 at 80iterations 3.3403574E-03 0.1006222 at 90iterations 1.4225631E-03 4.3373108E-02 at 100iterations 6.4321986E-04 2.2824287E-02 at 110iterations 3.2940551E-04 1.3047218E-02 at 120iterations finished qdiffx linear iterations at : 17:04:12 total time elapsed so far: 9.870000 # loops : 120 mean,max change (kT/e) : 3.2940551E-04 1.3047218E-02 energy calculations done at 9.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.09000 DelPhi exited at 17:04:14 10.096u 0.234s 0:12.08 85.4% 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 17:04:14 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: 326 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4805 !!! WARNING: GLM 171 has a net charge of -0.0940 !!! WARNING: HEM 821 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.307127 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): -18.72500 36.71400 ymin,ymax (A): -30.65200 34.29400 zmin,zma (A): -3.969000 65.46800 x,y,z range (A): 55.43900 64.94600 69.43700 scale (grids/A): 2.307127 object centre (A): 8.994500 1.821001 30.74950 number of atom coordinates read : 4805 total number of charged atoms : 4555 net assigned charge : 9.706057 assigned positive charge : 722.5015 centred at (gu) : 91.07236 92.73097 82.35920 assigned negative charge : -712.7997 centred at (gu) : 90.62345 92.95414 82.20442 start vw surface at 0.2100000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 212577 reading accessible surface arcs data from file ARCDAT no. of arc points read = 42935 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 94806 mr = 153364 m= 23768 mr = 73630 m= 3201 mr = 16862 m= 148 mr = 1909 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.9999999 no. cavity mid-points inaccessible to solvent = 456 time to turn everything in is 1.700000 number of dielectric boundary points 88691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 36358 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) : 1.538085 object centre at (A) : 8.994500 1.821001 30.74950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1212143 0.4971515 midg,1,midg; midg,igrid,midg 0.1404906 -0.2409216 1,midg,midg; igrid,midg,midg -6.5960124E-04 0.1822274 gauss-seidel spectral radius is 0.9991716 estimated iterations to convergence 274 setup time was (sec) 2.110000 now iterating at: 17:04:16 rms-change max change #iterations 10.44959 286.4629 at 10iterations 6.041678 159.2065 at 20iterations 3.454622 78.33819 at 30iterations 1.967628 48.20107 at 40iterations 1.111927 23.20858 at 50iterations 0.6279647 14.41907 at 60iterations 0.3542061 6.941479 at 70iterations 0.1984955 4.052797 at 80iterations 0.1114320 2.218204 at 90iterations 6.2379833E-02 1.250538 at 100iterations 3.4865171E-02 0.6445026 at 110iterations 1.9496262E-02 0.4399567 at 120iterations 1.0891168E-02 0.2217150 at 130iterations 6.0842182E-03 0.1196156 at 140iterations 3.3993265E-03 6.4312935E-02 at 150iterations 1.8992608E-03 3.4423828E-02 at 160iterations 1.0651038E-03 2.1813393E-02 at 170iterations 6.0314953E-04 1.1444092E-02 at 180iterations finished qdiffx linear iterations at : 17:04:28 total time elapsed so far: 14.20000 # loops : 180 mean,max change (kT/e) : 6.0314953E-04 1.1444092E-02 energy calculations done at 14.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.39000 DelPhi exited at 17:04:29 14.394u 0.235s 0:14.96 97.7% 0+0k 0+0io 0pf+0w