Tue Oct 11 03:35:37 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 Tue Oct 11 2011 at 03:35:37 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 = 2196 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: 0.6344680 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): -1.707000 46.67100 ymin,ymax (A): -15.91100 32.81400 zmin,zma (A): 39.28200 95.39200 x,y,z range (A): 48.37800 48.72500 56.11000 scale (grids/A): 0.6344680 object centre (A): 22.48200 8.451500 67.33700 number of atom coordinates read : 2196 total number of charged atoms : 2064 net assigned charge : -5.999984 assigned positive charge : 317.2655 centred at (gu) : 89.52778 89.32068 89.17424 assigned negative charge : -323.2658 centred at (gu) : 89.56805 89.50985 89.19531 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5701 nv = 96 ne = 84 npr = 46900 no. pairs analyzed = 46900 no. exposed pairs = 2826 no. arc points = 19801 no. surface atoms = 956 nbur = 1240 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 295 mr = 2919 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.2800000 number of dielectric boundary points 3043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1886 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7030 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8956516E-09 -7.8498550E-09 midg,1,midg; midg,igrid,midg 9.2281836E-09 -2.0457396E-08 1,midg,midg; igrid,midg,midg -4.6443920E-09 -9.9056781E-09 gauss-seidel spectral radius is 0.9870960 estimated iterations to convergence 72 setup time was (sec) 0.5200000 now iterating at: 03:35:37 rms-change max change #iterations 0.1303436 20.59193 at 10iterations 1.2496674E-02 2.200485 at 20iterations 1.1700664E-03 0.1724701 at 30iterations 1.1486872E-04 1.8180847E-02 at 40iterations 1.1360322E-05 1.8806458E-03 at 50iterations finished qdiffx linear iterations at : 03:35:40 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.1360322E-05 1.8806458E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 03:35:42 3.411u 0.177s 0:05.11 70.0% 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 Tue Oct 11 2011 at 03:35:42 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 = 2196 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.903404 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): -1.707000 46.67100 ymin,ymax (A): -15.91100 32.81400 zmin,zma (A): 39.28200 95.39200 x,y,z range (A): 48.37800 48.72500 56.11000 scale (grids/A): 1.903404 object centre (A): 22.48200 8.451500 67.33700 number of atom coordinates read : 2196 total number of charged atoms : 2064 net assigned charge : -5.999984 assigned positive charge : 317.2655 centred at (gu) : 88.58296 87.96169 87.52222 assigned negative charge : -323.2658 centred at (gu) : 88.70415 88.52943 87.58585 start vw surface at 0.1900000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 61212 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19801 grid for indexing accessible points = 1.400000 m= 21214 mr = 40677 m= 3332 mr = 15088 m= 185 mr = 1933 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 920 time to turn everything in is 0.5300000 number of dielectric boundary points 28197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 16243 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) : 0.6344680 object centre at (A) : 22.48200 8.451500 67.33700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2402563E-03 -2.8207613E-02 midg,1,midg; midg,igrid,midg 1.5053391E-02 -3.8433876E-02 1,midg,midg; igrid,midg,midg -1.4200929E-03 -1.3593157E-02 gauss-seidel spectral radius is 0.9985918 estimated iterations to convergence 211 setup time was (sec) 0.8200000 now iterating at: 03:35:43 rms-change max change #iterations 3.796982 164.6054 at 10iterations 1.750278 66.83454 at 20iterations 0.8093598 30.80002 at 30iterations 0.3746679 13.26284 at 40iterations 0.1736410 6.317521 at 50iterations 8.0175050E-02 2.629785 at 60iterations 3.7099794E-02 1.265503 at 70iterations 1.7171454E-02 0.5373955 at 80iterations 7.9310639E-03 0.2795830 at 90iterations 3.6629369E-03 0.1202850 at 100iterations 1.6976114E-03 5.5973053E-02 at 110iterations 7.8475568E-04 2.6674271E-02 at 120iterations finished qdiffx linear iterations at : 03:35:49 total time elapsed so far: 7.190000 # loops : 120 mean,max change (kT/e) : 7.8475568E-04 2.6674271E-02 energy calculations done at 7.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.420000 DelPhi exited at 03:35:50 7.419u 0.173s 0:08.39 90.3% 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 Tue Oct 11 2011 at 03:35:50 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 = 2196 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: 2.855106 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): -1.707000 46.67100 ymin,ymax (A): -15.91100 32.81400 zmin,zma (A): 39.28200 95.39200 x,y,z range (A): 48.37800 48.72500 56.11000 scale (grids/A): 2.855106 object centre (A): 22.48200 8.451500 67.33700 number of atom coordinates read : 2196 total number of charged atoms : 2064 net assigned charge : -5.999984 assigned positive charge : 317.2655 centred at (gu) : 87.87437 86.94246 86.28341 assigned negative charge : -323.2658 centred at (gu) : 88.05627 87.79414 86.37880 start vw surface at 0.1400000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 141460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19801 grid for indexing accessible points = 1.400000 m= 68233 mr = 99214 m= 24858 mr = 54282 m= 5922 mr = 19434 m= 786 mr = 4179 m= 40 mr = 510 m= 0 mr = 7 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 2979 time to turn everything in is 1.210000 number of dielectric boundary points 63673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 16512 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) : 1.903404 object centre at (A) : 22.48200 8.451500 67.33700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1043693E-02 -0.2370487 midg,1,midg; midg,igrid,midg 0.2472004 -0.3675694 1,midg,midg; igrid,midg,midg 0.1036055 -9.6544638E-02 gauss-seidel spectral radius is 0.9992432 estimated iterations to convergence 287 setup time was (sec) 1.520000 now iterating at: 03:35:52 rms-change max change #iterations 8.888894 400.8896 at 10iterations 5.103924 121.7562 at 20iterations 2.919097 59.72462 at 30iterations 1.666133 38.39866 at 40iterations 0.9495928 19.68004 at 50iterations 0.5413680 10.89158 at 60iterations 0.3084985 5.997534 at 70iterations 0.1758923 3.641654 at 80iterations 0.1000803 2.016685 at 90iterations 5.6967482E-02 1.131392 at 100iterations 3.2468304E-02 0.6389313 at 110iterations 1.8483110E-02 0.3905544 at 120iterations 1.0544295E-02 0.1981859 at 130iterations 5.9871171E-03 0.1229553 at 140iterations 3.4205706E-03 7.2869301E-02 at 150iterations 1.9499693E-03 3.7606239E-02 at 160iterations 1.1114022E-03 2.1196365E-02 at 170iterations 6.3481653E-04 1.2763977E-02 at 180iterations finished qdiffx linear iterations at : 03:36:02 total time elapsed so far: 11.77000 # loops : 180 mean,max change (kT/e) : 6.3481653E-04 1.2763977E-02 energy calculations done at 11.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 03:36:03 11.958u 0.175s 0:12.51 96.8% 0+0k 0+0io 0pf+0w