Tue Nov 22 14:14:10 PST 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+sph2.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 = amb2.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 Nov 22 2011 at 14:14:16 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 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: 0.5979073 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): -24.50600 35.03500 ymin,ymax (A): -19.37700 20.71800 zmin,zma (A): -2.736000 38.78700 x,y,z range (A): 59.54100 40.09500 41.52300 scale (grids/A): 0.5979073 object centre (A): 5.264500 0.6705008 18.02550 number of atom coordinates read : 2136 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 89.78268 90.27150 90.19476 assigned negative charge : -288.0262 centred at (gu) : 89.78152 90.36195 90.33183 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4778 nv = 96 ne = 84 npr = 39691 no. pairs analyzed = 39691 no. exposed pairs = 2419 no. arc points = 17178 no. surface atoms = 812 nbur = 1324 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 183 mr = 2613 m= 2 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.2100000 number of dielectric boundary points 2342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1777 ## 210 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5808 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.4421711E-09 -2.4268847E-09 midg,1,midg; midg,igrid,midg 3.2825485E-09 -1.1773997E-09 1,midg,midg; igrid,midg,midg 1.2481749E-09 1.1902950E-09 gauss-seidel spectral radius is 0.9854717 estimated iterations to convergence 68 setup time was (sec) 0.4400000 now iterating at: 14:14:20 rms-change max change #iterations 9.2303902E-02 16.55458 at 10iterations 7.7363574E-03 1.314171 at 20iterations 6.4669229E-04 0.1322098 at 30iterations 5.4413023E-05 9.4680786E-03 at 40iterations 4.5217967E-06 7.6675415E-04 at 50iterations finished qdiffx linear iterations at : 14:14:27 total time elapsed so far: 2.870000 # loops : 50 mean,max change (kT/e) : 4.5217967E-06 7.6675415E-04 energy calculations done at 2.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 14:14:29 3.052u 0.152s 0:14.00 22.8% 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 Nov 22 2011 at 14:14:31 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 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: 1.793722 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): -24.50600 35.03500 ymin,ymax (A): -19.37700 20.71800 zmin,zma (A): -2.736000 38.78700 x,y,z range (A): 59.54100 40.09500 41.52300 scale (grids/A): 1.793722 object centre (A): 5.264500 0.6705008 18.02550 number of atom coordinates read : 2136 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 89.34796 90.81429 90.58411 assigned negative charge : -288.0262 centred at (gu) : 89.34472 91.08591 90.99569 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 51895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17178 grid for indexing accessible points = 1.400000 m= 18239 mr = 35612 m= 2238 mr = 13851 m= 71 mr = 1366 m= 0 mr = 16 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 896 time to turn everything in is 0.3500000 number of dielectric boundary points 21598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 171 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 14283 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) : 0.5979073 object centre at (A) : 5.264500 0.6705008 18.02550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.4002772E-03 -4.5816274E-03 midg,1,midg; midg,igrid,midg 3.7569276E-03 -2.1341802E-03 1,midg,midg; igrid,midg,midg 2.9904705E-02 2.3387279E-02 gauss-seidel spectral radius is 0.9983873 estimated iterations to convergence 198 setup time was (sec) 0.6200000 now iterating at: 14:14:37 rms-change max change #iterations 3.183109 157.3956 at 10iterations 1.391642 61.38161 at 20iterations 0.6098890 23.68042 at 30iterations 0.2672297 10.26870 at 40iterations 0.1167874 4.061549 at 50iterations 5.1421370E-02 1.921928 at 60iterations 2.2497425E-02 0.8602409 at 70iterations 9.8604308E-03 0.4281921 at 80iterations 4.3158401E-03 0.1877136 at 90iterations 1.8923501E-03 8.9328766E-02 at 100iterations 8.2926679E-04 3.2093048E-02 at 110iterations 3.6403895E-04 1.4513016E-02 at 120iterations finished qdiffx linear iterations at : 14:14:55 total time elapsed so far: 6.670000 # loops : 120 mean,max change (kT/e) : 3.6403895E-04 1.4513016E-02 energy calculations done at 6.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.840000 DelPhi exited at 14:14:58 6.845u 0.204s 0:27.00 26.0% 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 Nov 22 2011 at 14:15:00 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2136 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: 2.690583 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): -24.50600 35.03500 ymin,ymax (A): -19.37700 20.71800 zmin,zma (A): -2.736000 38.78700 x,y,z range (A): 59.54100 40.09500 41.52300 scale (grids/A): 2.690583 object centre (A): 5.264500 0.6705008 18.02550 number of atom coordinates read : 2136 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.0260 centred at (gu) : 89.02190 91.22149 90.87611 assigned negative charge : -288.0262 centred at (gu) : 89.01712 91.62886 91.49347 start vw surface at 0.1100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 120035 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17178 grid for indexing accessible points = 1.400000 m= 60392 mr = 86392 m= 20205 mr = 50035 m= 3856 mr = 16582 m= 281 mr = 2888 m= 5 mr = 152 m= 0 mr = 2 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 3111 time to turn everything in is 0.8500000 number of dielectric boundary points 48723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 14651 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) : 1.793722 object centre at (A) : 5.264500 0.6705008 18.02550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.7493645E-02 -3.5078261E-02 midg,1,midg; midg,igrid,midg 2.8096076E-02 -1.6780540E-02 1,midg,midg; igrid,midg,midg 0.3268823 0.1926231 gauss-seidel spectral radius is 0.9991698 estimated iterations to convergence 274 setup time was (sec) 1.120000 now iterating at: 14:15:07 rms-change max change #iterations 7.756050 265.9063 at 10iterations 4.365194 168.0749 at 20iterations 2.444911 65.33701 at 30iterations 1.358883 32.75972 at 40iterations 0.7553360 22.47115 at 50iterations 0.4196517 9.655358 at 60iterations 0.2336974 5.707139 at 70iterations 0.1296334 2.885620 at 80iterations 7.1682565E-02 1.642442 at 90iterations 3.9909456E-02 0.9384413 at 100iterations 2.2151418E-02 0.4733715 at 110iterations 1.2277429E-02 0.2460371 at 120iterations 6.7952233E-03 0.1424866 at 130iterations 3.7626119E-03 8.5430145E-02 at 140iterations 2.0930793E-03 4.7876596E-02 at 150iterations 1.1621451E-03 2.5961876E-02 at 160iterations 6.4194686E-04 1.3499498E-02 at 170iterations 3.5625324E-04 8.6479187E-03 at 180iterations finished qdiffx linear iterations at : 14:15:37 total time elapsed so far: 10.61000 # loops : 180 mean,max change (kT/e) : 3.5625324E-04 8.6479187E-03 energy calculations done at 10.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.78000 DelPhi exited at 14:15:42 10.785u 0.160s 0:42.25 25.8% 0+0k 0+0io 0pf+0w