Wed Feb 15 08:56:26 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:26 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 = 4747 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5135084 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): 3.229000 67.30600 ymin,ymax (A): -0.8649999 54.17100 zmin,zma (A): -35.96100 33.36600 x,y,z range (A): 64.07700 55.03600 69.32700 scale (grids/A): 0.5135084 object centre (A): 35.26750 26.65300 -1.297501 number of atom coordinates read : 4747 total number of charged atoms : 4592 net assigned charge : 7.500048 assigned positive charge : 718.1699 centred at (gu) : 89.85356 90.59117 91.17284 assigned negative charge : -710.6746 centred at (gu) : 89.93028 90.66740 91.06808 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 7785 nv = 96 ne = 84 npr = 98147 no. pairs analyzed = 98147 no. exposed pairs = 5682 no. arc points = 39040 no. surface atoms = 1915 nbur = 2832 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 = 1.680000 m= 265 mr = 4182 m= 0 mr = 7 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.5200000 number of dielectric boundary points 3861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3917 ## 592 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 10599 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3930049E-10 5.7252453E-10 midg,1,midg; midg,igrid,midg 2.9004585E-10 -1.2558450E-10 1,midg,midg; igrid,midg,midg 3.5317946E-10 -1.0352388E-10 gauss-seidel spectral radius is 0.9805949 estimated iterations to convergence 59 setup time was (sec) 0.7500000 now iterating at: 08:56:27 rms-change max change #iterations 7.0987448E-02 11.13296 at 10iterations 5.4461109E-03 0.8526139 at 20iterations 1.3063372E-03 0.1841927 at 30iterations 5.2391714E-04 8.0490112E-02 at 40iterations 2.2125665E-04 3.5306931E-02 at 50iterations finished qdiffx linear iterations at : 08:56:30 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 2.2125665E-04 3.5306931E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 08:56:31 3.608u 0.162s 0:04.83 77.8% 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 Wed Feb 15 2012 at 08:56:31 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 = 4747 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: 1.540525 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): 3.229000 67.30600 ymin,ymax (A): -0.8649999 54.17100 zmin,zma (A): -35.96100 33.36600 x,y,z range (A): 64.07700 55.03600 69.32700 scale (grids/A): 1.540525 object centre (A): 35.26750 26.65300 -1.297501 number of atom coordinates read : 4747 total number of charged atoms : 4592 net assigned charge : 7.500048 assigned positive charge : 718.1699 centred at (gu) : 89.55933 91.77221 93.51721 assigned negative charge : -710.6746 centred at (gu) : 89.79041 92.00155 93.20407 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 88874 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39040 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25146 mr = 62213 m= 1978 mr = 16771 m= 40 mr = 882 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 343 time to turn everything in is 0.6500000 number of dielectric boundary points 36172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 558 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 34563 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) : 0.5135084 object centre at (A) : 35.26750 26.65300 -1.297501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3410950E-02 3.5708584E-02 midg,1,midg; midg,igrid,midg 9.0892566E-03 -1.9172663E-03 1,midg,midg; igrid,midg,midg 2.2716155E-02 -2.1788636E-03 gauss-seidel spectral radius is 0.9981229 estimated iterations to convergence 183 setup time was (sec) 0.9500000 now iterating at: 08:56:32 rms-change max change #iterations 3.789142 144.2200 at 10iterations 1.552011 60.59320 at 20iterations 0.6418787 19.77044 at 30iterations 0.2630842 8.492118 at 40iterations 0.1089968 3.758499 at 50iterations 4.4938516E-02 1.424881 at 60iterations 1.8698527E-02 0.5924797 at 70iterations 7.9527674E-03 0.2693362 at 80iterations 3.5773248E-03 0.1216393 at 90iterations 1.7792135E-03 5.8592796E-02 at 100iterations 1.0254103E-03 3.7296295E-02 at 110iterations 6.6480838E-04 2.1537781E-02 at 120iterations finished qdiffx linear iterations at : 08:56:39 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 6.6480838E-04 2.1537781E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.020000 DelPhi exited at 08:56:40 8.027u 0.231s 0:08.60 95.9% 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 Wed Feb 15 2012 at 08:56:40 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 = 4747 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: 2.310788 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): 3.229000 67.30600 ymin,ymax (A): -0.8649999 54.17100 zmin,zma (A): -35.96100 33.36600 x,y,z range (A): 64.07700 55.03600 69.32700 scale (grids/A): 2.310788 object centre (A): 35.26750 26.65300 -1.297501 number of atom coordinates read : 4747 total number of charged atoms : 4592 net assigned charge : 7.500048 assigned positive charge : 718.1699 centred at (gu) : 89.33866 92.65794 95.27524 assigned negative charge : -710.6746 centred at (gu) : 89.68544 93.00243 94.80618 start vw surface at 0.2100000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 207716 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39040 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 91058 mr = 152842 m= 22135 mr = 71580 m= 2842 mr = 16130 m= 144 mr = 1774 m= 4 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.9300001 no. cavity mid-points inaccessible to solvent = 1212 time to turn everything in is 1.590000 number of dielectric boundary points 81516 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 36645 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) : 1.540525 object centre at (A) : 35.26750 26.65300 -1.297501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2318170 0.6186342 midg,1,midg; midg,igrid,midg 0.1281940 -4.0219840E-02 1,midg,midg; igrid,midg,midg 0.4096370 -1.4198627E-03 gauss-seidel spectral radius is 0.9991603 estimated iterations to convergence 273 setup time was (sec) 1.950000 now iterating at: 08:56:42 rms-change max change #iterations 10.23190 272.6121 at 10iterations 5.873017 141.8480 at 20iterations 3.347408 78.33517 at 30iterations 1.890482 40.25769 at 40iterations 1.066914 23.58730 at 50iterations 0.5988180 13.97846 at 60iterations 0.3354062 7.144705 at 70iterations 0.1875322 3.674248 at 80iterations 0.1048164 2.135088 at 90iterations 5.8584373E-02 1.058185 at 100iterations 3.2612942E-02 0.7219639 at 110iterations 1.8196642E-02 0.3272018 at 120iterations 1.0156527E-02 0.1982956 at 130iterations 5.6905192E-03 0.1128769 at 140iterations 3.1960038E-03 5.7033539E-02 at 150iterations 1.8130013E-03 3.4121513E-02 at 160iterations 1.0476165E-03 2.0812988E-02 at 170iterations 6.2173256E-04 1.2067795E-02 at 180iterations finished qdiffx linear iterations at : 08:56:55 total time elapsed so far: 14.90000 # loops : 180 mean,max change (kT/e) : 6.2173256E-04 1.2067795E-02 energy calculations done at 14.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.12000 DelPhi exited at 08:56:56 15.121u 0.256s 0:15.79 97.3% 0+0k 0+0io 0pf+0w