Mon Oct 10 17:02:56 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 17:02:56 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: LYS 121 has a net charge of 1.5000 !!! WARNING: HIR 148 has a net charge of 0.5140 !!! WARNING: PRO 352 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5443175 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): -34.93200 30.47100 ymin,ymax (A): -22.35500 26.06400 zmin,zma (A): -1.044000 46.74400 x,y,z range (A): 65.40300 48.41900 47.78800 scale (grids/A): 0.5443175 object centre (A): -2.230502 1.854500 22.85000 number of atom coordinates read : 2986 total number of charged atoms : 2845 net assigned charge : -1.471974 assigned positive charge : 448.7460 centred at (gu) : 89.65289 89.83870 90.49559 assigned negative charge : -450.2191 centred at (gu) : 89.59026 89.71442 90.60123 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5662 nv = 96 ne = 84 npr = 59970 no. pairs analyzed = 59970 no. exposed pairs = 3940 no. arc points = 27924 no. surface atoms = 1327 nbur = 1659 mkacc time = 0.1300000 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 = 1.596000 m= 201 mr = 2772 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2789 ## 401 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7518 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1256649E-10 -8.5587132E-10 midg,1,midg; midg,igrid,midg -9.1302832E-10 6.6777156E-10 1,midg,midg; igrid,midg,midg -5.2090399E-10 2.8812266E-10 gauss-seidel spectral radius is 0.9826041 estimated iterations to convergence 62 setup time was (sec) 0.5100000 now iterating at: 17:02:57 rms-change max change #iterations 7.2406925E-02 13.70136 at 10iterations 4.6877316E-03 0.7099171 at 20iterations 3.1144996E-04 4.5412064E-02 at 30iterations 2.1104339E-05 3.0326843E-03 at 40iterations 1.5735891E-06 3.2806396E-04 at 50iterations finished qdiffx linear iterations at : 17:02:59 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 1.5735891E-06 3.2806396E-04 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 17:03:00 3.098u 0.155s 0:03.85 84.1% 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 17:03:00 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: LYS 121 has a net charge of 1.5000 !!! WARNING: HIR 148 has a net charge of 0.5140 !!! WARNING: PRO 352 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.632953 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): -34.93200 30.47100 ymin,ymax (A): -22.35500 26.06400 zmin,zma (A): -1.044000 46.74400 x,y,z range (A): 65.40300 48.41900 47.78800 scale (grids/A): 1.632953 object centre (A): -2.230502 1.854500 22.85000 number of atom coordinates read : 2986 total number of charged atoms : 2845 net assigned charge : -1.471974 assigned positive charge : 448.7460 centred at (gu) : 88.95782 89.51515 91.48595 assigned negative charge : -450.2191 centred at (gu) : 88.77037 89.14304 91.80338 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 63320 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27924 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18127 mr = 41617 m= 1700 mr = 12085 m= 33 mr = 748 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 343 time to turn everything in is 0.4500000 number of dielectric boundary points 28728 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 325 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 21758 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) : 0.5443175 object centre at (A) : -2.230502 1.854500 22.85000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5636669E-03 -3.2648256E-03 midg,1,midg; midg,igrid,midg -1.3539804E-02 6.8149716E-03 1,midg,midg; igrid,midg,midg -2.2018688E-02 -9.1900546E-03 gauss-seidel spectral radius is 0.9981865 estimated iterations to convergence 187 setup time was (sec) 0.7200000 now iterating at: 17:03:01 rms-change max change #iterations 3.314403 154.2898 at 10iterations 1.374729 52.35099 at 20iterations 0.5729614 22.79841 at 30iterations 0.2381033 8.496196 at 40iterations 9.9374071E-02 3.796298 at 50iterations 4.1275110E-02 1.590165 at 60iterations 1.7201357E-02 0.6497257 at 70iterations 7.1584801E-03 0.2368448 at 80iterations 3.0005190E-03 0.1039804 at 90iterations 1.2491856E-03 4.8404694E-02 at 100iterations 5.1933690E-04 2.0656586E-02 at 110iterations 2.1682921E-04 8.4724426E-03 at 120iterations finished qdiffx linear iterations at : 17:03:07 total time elapsed so far: 6.580000 # loops : 120 mean,max change (kT/e) : 2.1682921E-04 8.4724426E-03 energy calculations done at 6.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.760000 DelPhi exited at 17:03:08 6.760u 0.164s 0:07.73 89.5% 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 17:03:08 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2986 !!! WARNING: HIT 107 has a net charge of 0.5140 !!! WARNING: LYS 121 has a net charge of 1.5000 !!! WARNING: HIR 148 has a net charge of 0.5140 !!! WARNING: PRO 352 has a net charge of 0.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.449429 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): -34.93200 30.47100 ymin,ymax (A): -22.35500 26.06400 zmin,zma (A): -1.044000 46.74400 x,y,z range (A): 65.40300 48.41900 47.78800 scale (grids/A): 2.449429 object centre (A): -2.230502 1.854500 22.85000 number of atom coordinates read : 2986 total number of charged atoms : 2845 net assigned charge : -1.471974 assigned positive charge : 448.7460 centred at (gu) : 88.43655 89.27255 92.22887 assigned negative charge : -450.2191 centred at (gu) : 88.15549 88.71452 92.70483 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 147076 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27924 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 64088 mr = 102477 m= 16944 mr = 49568 m= 2452 mr = 12330 m= 142 mr = 1478 m= 4 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 1160 time to turn everything in is 1.040000 number of dielectric boundary points 64789 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.160000 number of grid points assigned charge 22735 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) : 1.632953 object centre at (A) : -2.230502 1.854500 22.85000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9739188E-02 -3.0335331E-02 midg,1,midg; midg,igrid,midg -0.1986673 0.1181706 1,midg,midg; igrid,midg,midg -0.5331579 -0.2322251 gauss-seidel spectral radius is 0.9991424 estimated iterations to convergence 270 setup time was (sec) 1.310000 now iterating at: 17:03:10 rms-change max change #iterations 8.675549 258.3796 at 10iterations 4.856614 127.0949 at 20iterations 2.704894 84.14477 at 30iterations 1.506316 35.36816 at 40iterations 0.8320846 17.28639 at 50iterations 0.4612139 10.10025 at 60iterations 0.2543405 5.344299 at 70iterations 0.1402110 3.153519 at 80iterations 7.7188738E-02 1.815968 at 90iterations 4.2472731E-02 0.9948959 at 100iterations 2.3348469E-02 0.4769697 at 110iterations 1.2853831E-02 0.2760901 at 120iterations 7.0656380E-03 0.1494751 at 130iterations 3.8798712E-03 7.7793121E-02 at 140iterations 2.1382410E-03 4.6955109E-02 at 150iterations 1.1724071E-03 2.3210526E-02 at 160iterations 6.4314523E-04 1.3662338E-02 at 170iterations 3.5473480E-04 6.9828033E-03 at 180iterations finished qdiffx linear iterations at : 17:03:19 total time elapsed so far: 10.47000 # loops : 180 mean,max change (kT/e) : 3.5473480E-04 6.9828033E-03 energy calculations done at 10.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.65000 DelPhi exited at 17:03:22 10.653u 0.190s 0:13.94 77.7% 0+0k 0+0io 0pf+0w