Sat Oct 15 13:12:56 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+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 Sat Oct 15 2011 at 13:12:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3048 !!! WARNING: MG7 714 has a net charge of 1.4000 !!! WARNING: MG7 715 has a net charge of 1.4000 !!! WARNING: MG7 716 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6328214 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): -15.31800 37.64600 ymin,ymax (A): 3.930000 55.86700 zmin,zma (A): -35.58400 20.67200 x,y,z range (A): 52.96400 51.93700 56.25600 scale (grids/A): 0.6328214 object centre (A): 11.16400 29.89850 -7.456000 number of atom coordinates read : 3048 total number of charged atoms : 2903 net assigned charge : -1.299988 assigned positive charge : 453.7052 centred at (gu) : 90.45965 91.27221 89.30142 assigned negative charge : -455.0066 centred at (gu) : 90.42877 91.42088 89.22427 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8244 nv = 96 ne = 84 npr = 61587 no. pairs analyzed = 61587 no. exposed pairs = 3873 no. arc points = 27277 no. surface atoms = 1321 nbur = 1727 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 491 mr = 4496 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 4179 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2668 ## 250 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9959 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1585290E-08 6.2794512E-09 midg,1,midg; midg,igrid,midg 1.1447533E-08 -2.4048939E-08 1,midg,midg; igrid,midg,midg -4.2520467E-09 2.4612998E-09 gauss-seidel spectral radius is 0.9871087 estimated iterations to convergence 72 setup time was (sec) 0.4800000 now iterating at: 13:12:56 rms-change max change #iterations 0.1556639 21.03216 at 10iterations 1.5314735E-02 2.140892 at 20iterations 1.9988166E-03 0.3162766 at 30iterations 5.8814936E-04 9.2754364E-02 at 40iterations 2.4741158E-04 3.5457611E-02 at 50iterations finished qdiffx linear iterations at : 13:13:00 total time elapsed so far: 4.210000 # loops : 50 mean,max change (kT/e) : 2.4741158E-04 3.5457611E-02 energy calculations done at 4.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.350000 DelPhi exited at 13:13:01 4.355u 0.296s 0:04.92 94.3% 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 Sat Oct 15 2011 at 13:13:01 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 = 3048 !!! WARNING: MG7 714 has a net charge of 1.4000 !!! WARNING: MG7 715 has a net charge of 1.4000 !!! WARNING: MG7 716 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.898464 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): -15.31800 37.64600 ymin,ymax (A): 3.930000 55.86700 zmin,zma (A): -35.58400 20.67200 x,y,z range (A): 52.96400 51.93700 56.25600 scale (grids/A): 1.898464 object centre (A): 11.16400 29.89850 -7.456000 number of atom coordinates read : 3048 total number of charged atoms : 2903 net assigned charge : -1.299988 assigned positive charge : 453.7052 centred at (gu) : 91.37807 93.81575 87.90338 assigned negative charge : -455.0066 centred at (gu) : 91.28605 94.26244 87.67252 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 89356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27277 grid for indexing accessible points = 1.400000 m= 31966 mr = 62076 m= 5469 mr = 22957 m= 377 mr = 3366 m= 2 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 268 time to turn everything in is 0.4800000 number of dielectric boundary points 38618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 22779 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) : 0.6328214 object centre at (A) : 11.16400 29.89850 -7.456000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4014701E-02 2.7133249E-02 midg,1,midg; midg,igrid,midg -1.0979926E-03 -2.8959651E-02 1,midg,midg; igrid,midg,midg -1.8061697E-02 -1.1606207E-02 gauss-seidel spectral radius is 0.9986716 estimated iterations to convergence 217 setup time was (sec) 0.7800000 now iterating at: 13:13:02 rms-change max change #iterations 4.660146 171.1052 at 10iterations 2.203713 72.88081 at 20iterations 1.045464 30.27943 at 30iterations 0.4945516 14.74053 at 40iterations 0.2354091 7.042709 at 50iterations 0.1114492 3.318623 at 60iterations 5.2914314E-02 1.573921 at 70iterations 2.5183452E-02 0.7696042 at 80iterations 1.2022207E-02 0.3534288 at 90iterations 5.8320127E-03 0.1626434 at 100iterations 2.8988020E-03 8.2840919E-02 at 110iterations 1.5374981E-03 4.8561096E-02 at 120iterations finished qdiffx linear iterations at : 13:13:11 total time elapsed so far: 9.770000 # loops : 120 mean,max change (kT/e) : 1.5374981E-03 4.8561096E-02 energy calculations done at 9.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.900000 DelPhi exited at 13:13:11 9.906u 0.330s 0:10.61 96.4% 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 Sat Oct 15 2011 at 13:13:11 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 = 3048 !!! WARNING: MG7 714 has a net charge of 1.4000 !!! WARNING: MG7 715 has a net charge of 1.4000 !!! WARNING: MG7 716 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.847696 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): -15.31800 37.64600 ymin,ymax (A): 3.930000 55.86700 zmin,zma (A): -35.58400 20.67200 x,y,z range (A): 52.96400 51.93700 56.25600 scale (grids/A): 2.847696 object centre (A): 11.16400 29.89850 -7.456000 number of atom coordinates read : 3048 total number of charged atoms : 2903 net assigned charge : -1.299988 assigned positive charge : 453.7052 centred at (gu) : 92.06699 95.72341 86.85509 assigned negative charge : -455.0066 centred at (gu) : 91.92909 96.39349 86.50875 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 207319 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27277 grid for indexing accessible points = 1.400000 m= 103236 mr = 151191 m= 37834 mr = 83321 m= 9958 mr = 29807 m= 1675 mr = 7405 m= 82 mr = 1140 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 1026 time to turn everything in is 1.190000 number of dielectric boundary points 87213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 23223 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) : 1.898464 object centre at (A) : 11.16400 29.89850 -7.456000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2048991 0.7083740 midg,1,midg; midg,igrid,midg -0.1479950 -0.3268366 1,midg,midg; igrid,midg,midg -4.3986995E-02 -0.1462321 gauss-seidel spectral radius is 0.9992870 estimated iterations to convergence 295 setup time was (sec) 1.470000 now iterating at: 13:13:13 rms-change max change #iterations 11.01649 363.5012 at 10iterations 6.534610 158.1034 at 20iterations 3.844483 78.72571 at 30iterations 2.263203 53.00939 at 40iterations 1.328414 26.96485 at 50iterations 0.7756034 14.27186 at 60iterations 0.4535783 8.064705 at 70iterations 0.2642436 4.558357 at 80iterations 0.1544172 3.066044 at 90iterations 9.0027459E-02 1.568979 at 100iterations 5.2271239E-02 0.9316330 at 110iterations 3.0528173E-02 0.5250397 at 120iterations 1.7795989E-02 0.3027725 at 130iterations 1.0411854E-02 0.2108774 at 140iterations 6.1054858E-03 0.1104403 at 150iterations 3.6199617E-03 7.1317673E-02 at 160iterations 2.1921655E-03 4.3849945E-02 at 170iterations 1.3755478E-03 2.6069641E-02 at 180iterations finished qdiffx linear iterations at : 13:13:26 total time elapsed so far: 14.75000 # loops : 180 mean,max change (kT/e) : 1.3755478E-03 2.6069641E-02 energy calculations done at 14.75000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.89000 DelPhi exited at 13:13:27 14.891u 0.278s 0:15.48 97.9% 0+0k 0+0io 0pf+0w