Fri Jan 27 10:55:41 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.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 Fri Jan 27 2012 at 10:55:41 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 ! Automatically converted by prot2crg.py # of charge parameter records: 968 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: ADP 901 has a net charge of -2.0000 !!! WARNING: MG1 902 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5690265 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): -36.33800 21.65500 ymin,ymax (A): 39.28800 88.26900 zmin,zma (A): -3.904000 58.65900 x,y,z range (A): 57.99300 48.98100 62.56300 scale (grids/A): 0.5690265 object centre (A): -7.341500 63.77850 27.37750 number of atom coordinates read : 3133 total number of charged atoms : 2986 net assigned charge : -3.999984 assigned positive charge : 479.4707 centred at (gu) : 92.12347 89.98642 89.22987 assigned negative charge : -483.4717 centred at (gu) : 92.05611 90.02898 89.19134 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6503 nv = 96 ne = 84 npr = 64047 no. pairs analyzed = 64047 no. exposed pairs = 4078 no. arc points = 27685 no. surface atoms = 1377 nbur = 1756 mkacc time = 0.1100000 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 = 1.484000 m= 247 mr = 3337 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3405 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2866 ## 322 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8504 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4964360E-09 1.2942367E-11 midg,1,midg; midg,igrid,midg 8.6710278E-11 -1.3081438E-09 1,midg,midg; igrid,midg,midg -1.0463531E-09 8.4830581E-10 gauss-seidel spectral radius is 0.9840752 estimated iterations to convergence 65 setup time was (sec) 0.4300000 now iterating at: 10:55:42 rms-change max change #iterations 8.9819096E-02 14.02606 at 10iterations 6.6302493E-03 1.018322 at 20iterations 5.0147052E-04 6.9881439E-02 at 30iterations 3.7626305E-05 5.5713654E-03 at 40iterations 2.8331967E-06 4.5156479E-04 at 50iterations finished qdiffx linear iterations at : 10:55:45 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 2.8331967E-06 4.5156479E-04 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 10:55:45 3.531u 0.190s 0:04.10 90.7% 0+0k 0+0io 4pf+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 Fri Jan 27 2012 at 10:55:45 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 ! Automatically converted by prot2crg.py # of charge parameter records: 968 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: ADP 901 has a net charge of -2.0000 !!! WARNING: MG1 902 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.707079 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): -36.33800 21.65500 ymin,ymax (A): 39.28800 88.26900 zmin,zma (A): -3.904000 58.65900 x,y,z range (A): 57.99300 48.98100 62.56300 scale (grids/A): 1.707079 object centre (A): -7.341500 63.77850 27.37750 number of atom coordinates read : 3133 total number of charged atoms : 2986 net assigned charge : -3.999984 assigned positive charge : 479.4707 centred at (gu) : 96.36942 89.95861 87.68874 assigned negative charge : -483.4717 centred at (gu) : 96.16797 90.08625 87.57349 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27685 grid for indexing accessible points = 1.400000 m= 22051 mr = 48127 m= 2420 mr = 15194 m= 68 mr = 1163 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 756 time to turn everything in is 0.3500000 number of dielectric boundary points 31649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 252 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 23100 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) : 0.5690265 object centre at (A) : -7.341500 63.77850 27.37750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6358109E-04 -3.8096137E-02 midg,1,midg; midg,igrid,midg 1.3082621E-04 -4.2837113E-03 1,midg,midg; igrid,midg,midg -1.2880564E-02 -3.7213534E-03 gauss-seidel spectral radius is 0.9983543 estimated iterations to convergence 196 setup time was (sec) 0.5900000 now iterating at: 10:55:46 rms-change max change #iterations 3.855286 195.3633 at 10iterations 1.667446 55.79005 at 20iterations 0.7249063 23.00250 at 30iterations 0.3158870 11.42897 at 40iterations 0.1369222 4.563981 at 50iterations 5.9523176E-02 2.043958 at 60iterations 2.5923109E-02 0.8721466 at 70iterations 1.1273334E-02 0.3423786 at 80iterations 4.9113217E-03 0.1967931 at 90iterations 2.1266330E-03 7.5935364E-02 at 100iterations 9.2321157E-04 2.9903412E-02 at 110iterations 4.0384434E-04 1.3319016E-02 at 120iterations finished qdiffx linear iterations at : 10:55:53 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 4.0384434E-04 1.3319016E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.050000 DelPhi exited at 10:55:54 8.048u 0.237s 0:08.70 95.0% 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 Fri Jan 27 2012 at 10:55:54 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 ! Automatically converted by prot2crg.py # of charge parameter records: 968 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3133 !!! WARNING: ADP 901 has a net charge of -2.0000 !!! WARNING: MG1 902 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.560619 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): -36.33800 21.65500 ymin,ymax (A): 39.28800 88.26900 zmin,zma (A): -3.904000 58.65900 x,y,z range (A): 57.99300 48.98100 62.56300 scale (grids/A): 2.560619 object centre (A): -7.341500 63.77850 27.37750 number of atom coordinates read : 3133 total number of charged atoms : 2986 net assigned charge : -3.999984 assigned positive charge : 479.4707 centred at (gu) : 99.55396 89.93797 86.53277 assigned negative charge : -483.4717 centred at (gu) : 99.25200 90.12927 86.36003 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 166393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27685 grid for indexing accessible points = 1.400000 m= 75959 mr = 118370 m= 22377 mr = 59636 m= 3887 mr = 16973 m= 326 mr = 2499 m= 9 mr = 147 m= 0 mr = 2 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 2542 time to turn everything in is 0.8800000 number of dielectric boundary points 71324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 23882 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) : 1.707079 object centre at (A) : -7.341500 63.77850 27.37750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2212327E-02 -0.7852622 midg,1,midg; midg,igrid,midg 5.1867752E-03 -6.3475668E-02 1,midg,midg; igrid,midg,midg -0.1411481 7.2269351E-03 gauss-seidel spectral radius is 0.9991880 estimated iterations to convergence 277 setup time was (sec) 1.130000 now iterating at: 10:55:55 rms-change max change #iterations 9.559021 330.7733 at 10iterations 5.404990 123.4818 at 20iterations 3.030313 69.41226 at 30iterations 1.705060 35.03324 at 40iterations 0.9556603 21.45740 at 50iterations 0.5362844 11.99753 at 60iterations 0.2995039 5.562795 at 70iterations 0.1679055 3.628923 at 80iterations 9.3892612E-02 1.861214 at 90iterations 5.2398674E-02 1.102813 at 100iterations 2.9320059E-02 0.5597363 at 110iterations 1.6354846E-02 0.3241773 at 120iterations 9.1584204E-03 0.1678998 at 130iterations 5.1122783E-03 9.7473145E-02 at 140iterations 2.8564022E-03 6.9926262E-02 at 150iterations 1.5940629E-03 2.9829025E-02 at 160iterations 8.9096540E-04 1.8058777E-02 at 170iterations 4.9753685E-04 1.0007739E-02 at 180iterations finished qdiffx linear iterations at : 10:56:07 total time elapsed so far: 12.78000 # loops : 180 mean,max change (kT/e) : 4.9753685E-04 1.0007739E-02 energy calculations done at 12.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 10:56:07 12.917u 0.231s 0:13.73 95.7% 0+0k 0+0io 0pf+0w