Mon Oct 10 16:05:11 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 Mon Oct 10 2011 at 16:05:11 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 = 4791 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 0.5523319 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): 7.816000 62.69400 ymin,ymax (A): 52.19800 116.3810 zmin,zma (A): -35.31400 29.14000 x,y,z range (A): 54.87800 64.18301 64.45400 scale (grids/A): 0.5523319 object centre (A): 35.25500 84.28951 -3.087002 number of atom coordinates read : 4791 total number of charged atoms : 4632 net assigned charge : 2.000020 assigned positive charge : 721.1954 centred at (gu) : 89.62095 89.93246 91.35165 assigned negative charge : -719.2001 centred at (gu) : 89.58263 89.94138 91.35189 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9307 nv = 96 ne = 84 npr = 99318 no. pairs analyzed = 99318 no. exposed pairs = 5729 no. arc points = 38808 no. surface atoms = 1940 nbur = 2851 mkacc time = 0.2600000 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 = 1.568000 m= 387 mr = 5207 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 4471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3967 ## 500 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 12342 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1935986E-10 2.1770873E-10 midg,1,midg; midg,igrid,midg 2.8656047E-10 3.9019381E-11 1,midg,midg; igrid,midg,midg -3.9845971E-10 6.1815908E-10 gauss-seidel spectral radius is 0.9832242 estimated iterations to convergence 64 setup time was (sec) 0.8200000 now iterating at: 16:05:12 rms-change max change #iterations 0.1008660 14.99665 at 10iterations 7.8113377E-03 1.308037 at 20iterations 1.3781721E-03 0.2207088 at 30iterations 5.4838025E-04 7.6313019E-02 at 40iterations 2.3943659E-04 3.1240463E-02 at 50iterations finished qdiffx linear iterations at : 16:05:15 total time elapsed so far: 4.550000 # loops : 50 mean,max change (kT/e) : 2.3943659E-04 3.1240463E-02 energy calculations done at 4.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.720000 DelPhi exited at 16:05:16 4.729u 0.391s 0:05.51 92.7% 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 Mon Oct 10 2011 at 16:05:16 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 = 4791 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 1.656996 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): 7.816000 62.69400 ymin,ymax (A): 52.19800 116.3810 zmin,zma (A): -35.31400 29.14000 x,y,z range (A): 54.87800 64.18301 64.45400 scale (grids/A): 1.656996 object centre (A): 35.25500 84.28951 -3.087002 number of atom coordinates read : 4791 total number of charged atoms : 4632 net assigned charge : 2.000020 assigned positive charge : 721.1954 centred at (gu) : 88.86098 89.79558 94.05320 assigned negative charge : -719.2001 centred at (gu) : 88.74721 89.82359 94.05520 start vw surface at 0.1800000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 104240 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38808 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 33373 mr = 74558 m= 3722 mr = 23488 m= 119 mr = 1928 m= 0 mr = 13 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 2738 time to turn everything in is 0.8500000 number of dielectric boundary points 41467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 418 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 35602 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) : 0.5523319 object centre at (A) : 35.25500 84.28951 -3.087002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8425763E-02 8.3605591E-03 midg,1,midg; midg,igrid,midg 9.5305163E-03 1.5558112E-02 1,midg,midg; igrid,midg,midg -7.0337183E-04 6.3316692E-03 gauss-seidel spectral radius is 0.9984090 estimated iterations to convergence 199 setup time was (sec) 1.160000 now iterating at: 16:05:18 rms-change max change #iterations 4.511199 161.0583 at 10iterations 1.989338 68.24983 at 20iterations 0.8776403 26.63872 at 30iterations 0.3877562 13.16999 at 40iterations 0.1709382 4.777747 at 50iterations 7.5681724E-02 2.179093 at 60iterations 3.3599641E-02 0.9629469 at 70iterations 1.4885361E-02 0.4875917 at 80iterations 6.7189108E-03 0.1926575 at 90iterations 3.1209264E-03 8.6866379E-02 at 100iterations 1.5206285E-03 4.5047760E-02 at 110iterations 8.3098968E-04 2.6287079E-02 at 120iterations finished qdiffx linear iterations at : 16:05:28 total time elapsed so far: 10.90000 # loops : 120 mean,max change (kT/e) : 8.3098968E-04 2.6287079E-02 energy calculations done at 10.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.08000 DelPhi exited at 16:05:28 11.089u 0.432s 0:11.95 96.3% 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 16:05:28 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 = 4791 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 2.485493 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): 7.816000 62.69400 ymin,ymax (A): 52.19800 116.3810 zmin,zma (A): -35.31400 29.14000 x,y,z range (A): 54.87800 64.18301 64.45400 scale (grids/A): 2.485493 object centre (A): 35.25500 84.28951 -3.087002 number of atom coordinates read : 4791 total number of charged atoms : 4632 net assigned charge : 2.000020 assigned positive charge : 721.1954 centred at (gu) : 88.29096 89.69296 96.07928 assigned negative charge : -719.2001 centred at (gu) : 88.12076 89.73521 96.08265 start vw surface at 0.1700000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 242904 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38808 grid for indexing accessible points = 1.400000 m= 114994 mr = 182031 m= 33798 mr = 92141 m= 5883 mr = 25860 m= 442 mr = 4007 m= 11 mr = 227 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 9140 time to turn everything in is 2.100000 number of dielectric boundary points 93766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 2.250000 number of grid points assigned charge 37016 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) : 1.656996 object centre at (A) : 35.25500 84.28951 -3.087002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3129206 0.4277041 midg,1,midg; midg,igrid,midg 8.7275855E-02 0.3553638 1,midg,midg; igrid,midg,midg 2.0406721E-02 0.1062624 gauss-seidel spectral radius is 0.9992433 estimated iterations to convergence 287 setup time was (sec) 2.450000 now iterating at: 16:05:31 rms-change max change #iterations 11.57680 393.6917 at 10iterations 6.821692 172.0764 at 20iterations 3.996520 87.14963 at 30iterations 2.333739 47.83461 at 40iterations 1.356608 25.16644 at 50iterations 0.7869220 13.27045 at 60iterations 0.4549420 8.126150 at 70iterations 0.2617639 4.614253 at 80iterations 0.1510333 2.579529 at 90iterations 8.6874790E-02 1.612658 at 100iterations 4.9986526E-02 1.044525 at 110iterations 2.8686902E-02 0.4730873 at 120iterations 1.6516689E-02 0.2692709 at 130iterations 9.5369667E-03 0.1574650 at 140iterations 5.5356184E-03 0.1112385 at 150iterations 3.2539747E-03 5.2441835E-02 at 160iterations 1.9494143E-03 3.2142639E-02 at 170iterations 1.2144007E-03 1.9714355E-02 at 180iterations finished qdiffx linear iterations at : 16:05:49 total time elapsed so far: 20.73000 # loops : 180 mean,max change (kT/e) : 1.2144007E-03 1.9714355E-02 energy calculations done at 20.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.91000 DelPhi exited at 16:05:50 20.917u 0.494s 0:21.74 98.4% 0+0k 0+0io 0pf+0w