Mon Oct 10 14:09:39 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 14:09:40 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 = 2393 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: 0.6068975 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): 39.95900 98.61800 ymin,ymax (A): -5.010000 48.01700 zmin,zma (A): -0.8390000 43.81400 x,y,z range (A): 58.65900 53.02700 44.65300 scale (grids/A): 0.6068975 object centre (A): 69.28850 21.50350 21.48750 number of atom coordinates read : 2393 total number of charged atoms : 2256 net assigned charge : 1.000008 assigned positive charge : 364.2832 centred at (gu) : 90.43710 89.81086 90.84017 assigned negative charge : -363.2836 centred at (gu) : 90.58119 89.88485 90.65811 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5934 nv = 96 ne = 84 npr = 47565 no. pairs analyzed = 47565 no. exposed pairs = 3183 no. arc points = 21877 no. surface atoms = 1074 nbur = 1319 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 231 mr = 3030 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2700000 number of dielectric boundary points 3126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2245 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7321 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.0587886E-09 9.7249240E-09 midg,1,midg; midg,igrid,midg 3.7523797E-09 -2.5353197E-09 1,midg,midg; igrid,midg,midg 5.8666094E-09 -6.2845071E-09 gauss-seidel spectral radius is 0.9859310 estimated iterations to convergence 69 setup time was (sec) 0.4800000 now iterating at: 14:09:40 rms-change max change #iterations 0.1077397 18.26497 at 10iterations 9.3427747E-03 1.541443 at 20iterations 8.5054751E-04 0.1348476 at 30iterations 1.1245169E-04 2.0903826E-02 at 40iterations 3.2258180E-05 7.3945522E-03 at 50iterations finished qdiffx linear iterations at : 14:09:43 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 3.2258180E-05 7.3945522E-03 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 14:09:43 3.053u 0.140s 0:03.62 88.1% 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 14:09:43 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 = 2393 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.820692 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): 39.95900 98.61800 ymin,ymax (A): -5.010000 48.01700 zmin,zma (A): -0.8390000 43.81400 x,y,z range (A): 58.65900 53.02700 44.65300 scale (grids/A): 1.820692 object centre (A): 69.28850 21.50350 21.48750 number of atom coordinates read : 2393 total number of charged atoms : 2256 net assigned charge : 1.000008 assigned positive charge : 364.2832 centred at (gu) : 91.31074 89.43192 92.51994 assigned negative charge : -363.2836 centred at (gu) : 91.74339 89.65432 91.97404 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 64760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21877 grid for indexing accessible points = 1.400000 m= 20247 mr = 43540 m= 2195 mr = 13835 m= 90 mr = 1057 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 851 time to turn everything in is 0.4700000 number of dielectric boundary points 28854 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 179 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 17649 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) : 0.6068975 object centre at (A) : 69.28850 21.50350 21.48750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1155101E-03 1.9374354E-02 midg,1,midg; midg,igrid,midg 4.3171574E-03 -2.0998692E-02 1,midg,midg; igrid,midg,midg 2.7529554E-02 -4.3803837E-02 gauss-seidel spectral radius is 0.9984881 estimated iterations to convergence 204 setup time was (sec) 0.7300000 now iterating at: 14:09:44 rms-change max change #iterations 3.728139 196.1351 at 10iterations 1.661776 60.79355 at 20iterations 0.7475926 29.55104 at 30iterations 0.3338687 11.23435 at 40iterations 0.1503389 5.257805 at 50iterations 6.7789875E-02 2.430473 at 60iterations 3.0441491E-02 1.187122 at 70iterations 1.3620153E-02 0.4647713 at 80iterations 6.1730295E-03 0.2402573 at 90iterations 2.7668080E-03 9.7099304E-02 at 100iterations 1.2584856E-03 4.4956207E-02 at 110iterations 5.7798874E-04 2.1707535E-02 at 120iterations finished qdiffx linear iterations at : 14:09:50 total time elapsed so far: 7.010000 # loops : 120 mean,max change (kT/e) : 5.7798874E-04 2.1707535E-02 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.190000 DelPhi exited at 14:09:51 7.194u 0.169s 0:07.76 94.7% 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 14:09:51 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 = 2393 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.731039 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): 39.95900 98.61800 ymin,ymax (A): -5.010000 48.01700 zmin,zma (A): -0.8390000 43.81400 x,y,z range (A): 58.65900 53.02700 44.65300 scale (grids/A): 2.731039 object centre (A): 69.28850 21.50350 21.48750 number of atom coordinates read : 2393 total number of charged atoms : 2256 net assigned charge : 1.000008 assigned positive charge : 364.2832 centred at (gu) : 91.96589 89.14767 93.77969 assigned negative charge : -363.2836 centred at (gu) : 92.61504 89.48143 92.96098 start vw surface at 0.2100000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 150173 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21877 grid for indexing accessible points = 1.400000 m= 69815 mr = 106661 m= 20004 mr = 54903 m= 3485 mr = 14857 m= 377 mr = 2257 m= 17 mr = 186 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 2858 time to turn everything in is 1.150000 number of dielectric boundary points 65007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 18045 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) : 1.820692 object centre at (A) : 69.28850 21.50350 21.48750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8012103E-03 0.1680904 midg,1,midg; midg,igrid,midg 0.1324621 -0.3367969 1,midg,midg; igrid,midg,midg 0.3610643 -0.6757177 gauss-seidel spectral radius is 0.9992186 estimated iterations to convergence 282 setup time was (sec) 1.420000 now iterating at: 14:09:53 rms-change max change #iterations 9.031842 256.1220 at 10iterations 5.243047 155.1294 at 20iterations 3.016390 63.71562 at 30iterations 1.724408 39.97960 at 40iterations 0.9855220 21.84970 at 50iterations 0.5617458 11.94504 at 60iterations 0.3195120 6.848234 at 70iterations 0.1816324 4.179572 at 80iterations 0.1032969 2.198680 at 90iterations 5.8452569E-02 1.246925 at 100iterations 3.3161901E-02 0.7214146 at 110iterations 1.8820371E-02 0.3924677 at 120iterations 1.0644891E-02 0.2126024 at 130iterations 6.0247341E-03 0.1295013 at 140iterations 3.4132923E-03 7.2977066E-02 at 150iterations 1.9326564E-03 3.8631439E-02 at 160iterations 1.0947026E-03 2.2186279E-02 at 170iterations 6.2105962E-04 1.3172150E-02 at 180iterations finished qdiffx linear iterations at : 14:10:02 total time elapsed so far: 10.67000 # loops : 180 mean,max change (kT/e) : 6.2105962E-04 1.3172150E-02 energy calculations done at 10.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.86000 DelPhi exited at 14:10:02 10.859u 0.180s 0:11.35 97.1% 0+0k 0+0io 0pf+0w