Sat Oct 15 11:27:50 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 Sat Oct 15 2011 at 11:27:50 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 689 has a net charge of 1.4000 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: 0.6124204 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): -32.12400 17.63200 ymin,ymax (A): -23.56500 24.14100 zmin,zma (A): -12.56600 45.56400 x,y,z range (A): 49.75600 47.70600 58.13000 scale (grids/A): 0.6124204 object centre (A): -7.246000 0.2879992 16.49900 number of atom coordinates read : 2629 total number of charged atoms : 2484 net assigned charge : 3.500007 assigned positive charge : 396.4950 centred at (gu) : 88.75494 88.92928 89.64906 assigned negative charge : -392.9955 centred at (gu) : 88.65318 88.98589 89.55006 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6428 nv = 96 ne = 84 npr = 54987 no. pairs analyzed = 54987 no. exposed pairs = 3042 no. arc points = 21834 no. surface atoms = 1015 nbur = 1614 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 297 mr = 3568 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 181 time to turn everything in is 0.2000000 number of dielectric boundary points 3122 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2234 ## 241 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8062 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3536329E-09 6.9796298E-09 midg,1,midg; midg,igrid,midg 6.7480732E-09 -5.8235478E-10 1,midg,midg; igrid,midg,midg -4.3516439E-09 5.8363603E-09 gauss-seidel spectral radius is 0.9861938 estimated iterations to convergence 70 setup time was (sec) 0.4900000 now iterating at: 11:27:51 rms-change max change #iterations 0.1201134 19.03443 at 10iterations 1.0730899E-02 1.649775 at 20iterations 9.7445346E-04 0.1488686 at 30iterations 8.7365028E-05 1.1947632E-02 at 40iterations 7.8523153E-06 1.2695789E-03 at 50iterations finished qdiffx linear iterations at : 11:27:55 total time elapsed so far: 4.760000 # loops : 50 mean,max change (kT/e) : 7.8523153E-06 1.2695789E-03 energy calculations done at 4.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.890000 DelPhi exited at 11:27:56 4.890u 0.346s 0:05.60 93.3% 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 Sat Oct 15 2011 at 11:27:56 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 689 has a net charge of 1.4000 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: 1.837261 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): -32.12400 17.63200 ymin,ymax (A): -23.56500 24.14100 zmin,zma (A): -12.56600 45.56400 x,y,z range (A): 49.75600 47.70600 58.13000 scale (grids/A): 1.837261 object centre (A): -7.246000 0.2879992 16.49900 number of atom coordinates read : 2629 total number of charged atoms : 2484 net assigned charge : 3.500007 assigned positive charge : 396.4950 centred at (gu) : 86.26442 86.78738 88.94674 assigned negative charge : -392.9955 centred at (gu) : 85.95918 86.95743 88.65004 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 70372 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21834 grid for indexing accessible points = 1.400000 m= 23927 mr = 49275 m= 3159 mr = 17577 m= 154 mr = 1879 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 6147 time to turn everything in is 0.3900000 number of dielectric boundary points 28840 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 19470 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) : 0.6124204 object centre at (A) : -7.246000 0.2879992 16.49900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.6374936E-03 2.6174946E-02 midg,1,midg; midg,igrid,midg 1.3746114E-02 -1.5007058E-04 1,midg,midg; igrid,midg,midg -8.0649583E-03 2.9428177E-02 gauss-seidel spectral radius is 0.9985353 estimated iterations to convergence 207 setup time was (sec) 0.7300000 now iterating at: 11:27:57 rms-change max change #iterations 3.940220 167.1632 at 10iterations 1.800076 71.94765 at 20iterations 0.8181917 27.52593 at 30iterations 0.3742503 12.47555 at 40iterations 0.1705389 6.183773 at 50iterations 7.7935718E-02 2.735556 at 60iterations 3.5459518E-02 1.097683 at 70iterations 1.6164638E-02 0.5383062 at 80iterations 7.3767947E-03 0.2385569 at 90iterations 3.3540081E-03 0.1120033 at 100iterations 1.5339605E-03 5.0696373E-02 at 110iterations 6.9875864E-04 2.5436401E-02 at 120iterations finished qdiffx linear iterations at : 11:28:09 total time elapsed so far: 10.31000 # loops : 120 mean,max change (kT/e) : 6.9875864E-04 2.5436401E-02 energy calculations done at 10.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.44000 DelPhi exited at 11:28:10 10.441u 0.506s 0:14.68 74.5% 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 Sat Oct 15 2011 at 11:28:10 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2629 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 689 has a net charge of 1.4000 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: 2.755892 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): -32.12400 17.63200 ymin,ymax (A): -23.56500 24.14100 zmin,zma (A): -12.56600 45.56400 x,y,z range (A): 49.75600 47.70600 58.13000 scale (grids/A): 2.755892 object centre (A): -7.246000 0.2879992 16.49900 number of atom coordinates read : 2629 total number of charged atoms : 2484 net assigned charge : 3.500007 assigned positive charge : 396.4950 centred at (gu) : 84.39661 85.18099 88.41985 assigned negative charge : -392.9955 centred at (gu) : 83.93889 85.43625 87.97509 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 163098 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21834 grid for indexing accessible points = 1.400000 m= 80178 mr = 119430 m= 25893 mr = 65822 m= 5500 mr = 20595 m= 641 mr = 4033 m= 37 mr = 399 m= 0 mr = 13 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 21093 time to turn everything in is 0.9200000 number of dielectric boundary points 65055 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 19869 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) : 1.837261 object centre at (A) : -7.246000 0.2879992 16.49900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7356716E-02 0.3724283 midg,1,midg; midg,igrid,midg 0.1777673 -8.5511282E-03 1,midg,midg; igrid,midg,midg -5.9588131E-02 0.3617164 gauss-seidel spectral radius is 0.9992251 estimated iterations to convergence 284 setup time was (sec) 1.200000 now iterating at: 11:28:12 rms-change max change #iterations 9.388933 349.7365 at 10iterations 5.372094 141.2595 at 20iterations 3.051271 68.50268 at 30iterations 1.738142 39.92912 at 40iterations 0.9875807 21.54909 at 50iterations 0.5612551 10.45523 at 60iterations 0.3181032 6.407649 at 70iterations 0.1806967 3.370729 at 80iterations 0.1023519 2.050552 at 90iterations 5.8050595E-02 1.193802 at 100iterations 3.2888845E-02 0.6367116 at 110iterations 1.8644258E-02 0.3741436 at 120iterations 1.0579499E-02 0.2324334 at 130iterations 5.9904023E-03 0.1142569 at 140iterations 3.3913087E-03 6.6871643E-02 at 150iterations 1.9253052E-03 3.6865234E-02 at 160iterations 1.0916981E-03 2.0168304E-02 at 170iterations 6.2016840E-04 1.1919975E-02 at 180iterations finished qdiffx linear iterations at : 11:28:33 total time elapsed so far: 14.80000 # loops : 180 mean,max change (kT/e) : 6.2016840E-04 1.1919975E-02 energy calculations done at 14.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.94000 DelPhi exited at 11:28:33 14.941u 0.308s 0:23.05 66.1% 0+0k 0+0io 0pf+0w