Sun Oct 9 13:45:05 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 Sun Oct 9 2011 at 13:45:05 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 = 2333 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6905247 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): -7.055000 44.50000 ymin,ymax (A): -14.02800 35.33700 zmin,zma (A): 1.882000 45.89400 x,y,z range (A): 51.55500 49.36500 44.01200 scale (grids/A): 0.6905247 object centre (A): 18.72250 10.65450 23.88800 number of atom coordinates read : 2333 total number of charged atoms : 2195 net assigned charge : 6.500011 assigned positive charge : 353.7171 centred at (gu) : 89.69756 91.62404 90.52526 assigned negative charge : -347.2177 centred at (gu) : 89.71175 91.68204 90.58076 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7584 nv = 96 ne = 84 npr = 46429 no. pairs analyzed = 46429 no. exposed pairs = 2980 no. arc points = 20986 no. surface atoms = 999 nbur = 1334 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 466 mr = 4158 m= 3 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1959 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8522 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1781402E-08 1.7585300E-08 midg,1,midg; midg,igrid,midg 4.2502940E-08 2.0085711E-08 1,midg,midg; igrid,midg,midg 4.4648598E-08 2.9769406E-08 gauss-seidel spectral radius is 0.9891023 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 13:45:06 rms-change max change #iterations 0.1932928 26.03043 at 10iterations 2.2826631E-02 3.100206 at 20iterations 3.1973384E-03 0.4187431 at 30iterations 7.3848391E-04 0.1186600 at 40iterations 2.5338653E-04 4.1275024E-02 at 50iterations finished qdiffx linear iterations at : 13:45:09 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.5338653E-04 4.1275024E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 13:45:09 3.420u 0.175s 0:03.87 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 Sun Oct 9 2011 at 13:45:09 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 = 2333 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.071574 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): -7.055000 44.50000 ymin,ymax (A): -14.02800 35.33700 zmin,zma (A): 1.882000 45.89400 x,y,z range (A): 51.55500 49.36500 44.01200 scale (grids/A): 2.071574 object centre (A): 18.72250 10.65450 23.88800 number of atom coordinates read : 2333 total number of charged atoms : 2195 net assigned charge : 6.500011 assigned positive charge : 353.7171 centred at (gu) : 89.09224 94.87186 91.57515 assigned negative charge : -347.2177 centred at (gu) : 89.13493 95.04604 91.74206 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 80765 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20986 grid for indexing accessible points = 1.400000 m= 30737 mr = 56044 m= 5411 mr = 22593 m= 482 mr = 3391 m= 12 mr = 244 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 35135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 17401 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) : 0.6905247 object centre at (A) : 18.72250 10.65450 23.88800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1189348E-02 1.4843150E-02 midg,1,midg; midg,igrid,midg 1.3806188E-02 8.5503515E-03 1,midg,midg; igrid,midg,midg 5.3867038E-02 -2.3924142E-02 gauss-seidel spectral radius is 0.9988154 estimated iterations to convergence 230 setup time was (sec) 0.6100000 now iterating at: 13:45:10 rms-change max change #iterations 4.688863 219.8216 at 10iterations 2.299217 69.40585 at 20iterations 1.134215 38.94963 at 30iterations 0.5616398 17.12923 at 40iterations 0.2756533 8.594696 at 50iterations 0.1365048 3.848370 at 60iterations 6.7622468E-02 1.982049 at 70iterations 3.3406731E-02 0.9972267 at 80iterations 1.6676968E-02 0.4817829 at 90iterations 8.3697867E-03 0.2501450 at 100iterations 4.2795646E-03 0.1291237 at 110iterations 2.2734341E-03 7.3501587E-02 at 120iterations finished qdiffx linear iterations at : 13:45:17 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 2.2734341E-03 7.3501587E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 13:45:18 7.947u 0.214s 0:08.46 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 Sun Oct 9 2011 at 13:45:18 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 = 2333 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: 3.107361 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): -7.055000 44.50000 ymin,ymax (A): -14.02800 35.33700 zmin,zma (A): 1.882000 45.89400 x,y,z range (A): 51.55500 49.36500 44.01200 scale (grids/A): 3.107361 object centre (A): 18.72250 10.65450 23.88800 number of atom coordinates read : 2333 total number of charged atoms : 2195 net assigned charge : 6.500011 assigned positive charge : 353.7171 centred at (gu) : 88.63822 97.30763 92.36265 assigned negative charge : -347.2177 centred at (gu) : 88.70239 97.56898 92.61314 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 186096 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20986 grid for indexing accessible points = 1.400000 m= 97398 mr = 135146 m= 37288 mr = 79592 m= 9965 mr = 29989 m= 1953 mr = 7474 m= 233 mr = 1371 m= 4 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 79230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 17559 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) : 2.071574 object centre at (A) : 18.72250 10.65450 23.88800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4663105 3.4437206E-02 midg,1,midg; midg,igrid,midg 0.2196512 1.3672210E-02 1,midg,midg; igrid,midg,midg 0.6351530 -0.6261810 gauss-seidel spectral radius is 0.9992979 estimated iterations to convergence 298 setup time was (sec) 1.460000 now iterating at: 13:45:19 rms-change max change #iterations 10.60173 409.1012 at 10iterations 6.321662 139.1367 at 20iterations 3.748137 75.81034 at 30iterations 2.216190 39.94222 at 40iterations 1.313949 23.12375 at 50iterations 0.7720208 17.51773 at 60iterations 0.4551619 7.512629 at 70iterations 0.2673616 4.659674 at 80iterations 0.1569587 2.638367 at 90iterations 9.2231505E-02 1.669720 at 100iterations 5.4165520E-02 0.9158401 at 110iterations 3.1892881E-02 0.5754852 at 120iterations 1.8910779E-02 0.3413086 at 130iterations 1.1384302E-02 0.2080460 at 140iterations 6.9991411E-03 0.1343946 at 150iterations 4.4848798E-03 9.5823288E-02 at 160iterations 3.0410273E-03 6.2215805E-02 at 170iterations 2.1984079E-03 4.6760559E-02 at 180iterations finished qdiffx linear iterations at : 13:45:31 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 2.1984079E-03 4.6760559E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 13:45:31 13.017u 0.219s 0:13.49 97.9% 0+0k 0+0io 0pf+0w