Mon Oct 10 17:03:46 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+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 Mon Oct 10 2011 at 17:03:46 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3202 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: 0.5368237 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): 31.39700 88.61800 ymin,ymax (A): -8.132000 47.07300 zmin,zma (A): 76.82600 143.1420 x,y,z range (A): 57.22099 55.20500 66.31600 scale (grids/A): 0.5368237 object centre (A): 60.00750 19.47050 109.9840 number of atom coordinates read : 3202 total number of charged atoms : 3063 net assigned charge : 5.500041 assigned positive charge : 475.6654 centred at (gu) : 90.88361 90.20923 89.64835 assigned negative charge : -470.1667 centred at (gu) : 90.94552 90.20694 89.46474 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6101 nv = 96 ne = 84 npr = 61598 no. pairs analyzed = 61598 no. exposed pairs = 4456 no. arc points = 32200 no. surface atoms = 1481 nbur = 1721 mkacc time = 9.9999994E-02 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 = 1.596000 m= 258 mr = 2880 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3158 ## 410 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8040 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.5262740E-10 1.0382584E-09 midg,1,midg; midg,igrid,midg 2.2239381E-10 2.7023228E-10 1,midg,midg; igrid,midg,midg 4.4116891E-10 -8.3457137E-11 gauss-seidel spectral radius is 0.9821491 estimated iterations to convergence 62 setup time was (sec) 0.4000000 now iterating at: 17:03:46 rms-change max change #iterations 6.9707051E-02 11.88367 at 10iterations 4.4492409E-03 0.8452454 at 20iterations 2.8575520E-04 5.2570343E-02 at 30iterations 2.1296490E-05 3.4866333E-03 at 40iterations 2.4073381E-06 2.9850006E-04 at 50iterations finished qdiffx linear iterations at : 17:03:49 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.4073381E-06 2.9850006E-04 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 17:03:50 3.393u 0.169s 0:03.87 91.7% 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 17:03:50 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3202 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: 1.610471 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): 31.39700 88.61800 ymin,ymax (A): -8.132000 47.07300 zmin,zma (A): 76.82600 143.1420 x,y,z range (A): 57.22099 55.20500 66.31600 scale (grids/A): 1.610471 object centre (A): 60.00750 19.47050 109.9840 number of atom coordinates read : 3202 total number of charged atoms : 3063 net assigned charge : 5.500041 assigned positive charge : 475.6654 centred at (gu) : 92.64983 90.62659 88.94405 assigned negative charge : -470.1667 centred at (gu) : 92.83615 90.62046 88.39370 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 68193 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32200 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 20033 mr = 43622 m= 1938 mr = 13266 m= 55 mr = 827 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1642 time to turn everything in is 0.3300000 number of dielectric boundary points 32502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 367 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 23390 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) : 0.5368237 object centre at (A) : 60.00750 19.47050 109.9840 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7158607E-02 1.5239634E-02 midg,1,midg; midg,igrid,midg 5.0578350E-03 5.2359835E-03 1,midg,midg; igrid,midg,midg 6.9026365E-03 -8.8621741E-03 gauss-seidel spectral radius is 0.9981782 estimated iterations to convergence 186 setup time was (sec) 0.5300000 now iterating at: 17:03:50 rms-change max change #iterations 3.291209 146.7215 at 10iterations 1.369808 53.25611 at 20iterations 0.5685517 22.40368 at 30iterations 0.2357267 9.312958 at 40iterations 9.7865351E-02 3.660005 at 50iterations 4.0605012E-02 1.467415 at 60iterations 1.6918989E-02 0.6746712 at 70iterations 7.0406361E-03 0.2501602 at 80iterations 2.9141554E-03 0.1033154 at 90iterations 1.2134069E-03 4.8591137E-02 at 100iterations 5.0547504E-04 1.9140482E-02 at 110iterations 2.1132719E-04 7.3652267E-03 at 120iterations finished qdiffx linear iterations at : 17:03:57 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 2.1132719E-04 7.3652267E-03 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.620000 DelPhi exited at 17:04:00 7.623u 0.201s 0:09.89 79.0% 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 Mon Oct 10 2011 at 17:04:00 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: 269 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3202 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: 2.415707 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): 31.39700 88.61800 ymin,ymax (A): -8.132000 47.07300 zmin,zma (A): 76.82600 143.1420 x,y,z range (A): 57.22099 55.20500 66.31600 scale (grids/A): 2.415707 object centre (A): 60.00750 19.47050 109.9840 number of atom coordinates read : 3202 total number of charged atoms : 3063 net assigned charge : 5.500041 assigned positive charge : 475.6654 centred at (gu) : 93.97445 90.93992 88.41573 assigned negative charge : -470.1667 centred at (gu) : 94.25407 90.93058 87.59033 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 158370 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32200 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 69767 mr = 108083 m= 19291 mr = 53123 m= 2932 mr = 14068 m= 183 mr = 1773 m= 5 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 5225 time to turn everything in is 0.8100000 number of dielectric boundary points 73421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 24465 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) : 1.610471 object centre at (A) : 60.00750 19.47050 109.9840 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4025397 0.2318107 midg,1,midg; midg,igrid,midg 7.9262793E-02 7.4065559E-02 1,midg,midg; igrid,midg,midg 0.1317867 -0.1507925 gauss-seidel spectral radius is 0.9991544 estimated iterations to convergence 272 setup time was (sec) 1.040000 now iterating at: 17:04:01 rms-change max change #iterations 8.773298 282.8963 at 10iterations 4.965060 151.9340 at 20iterations 2.798724 78.61713 at 30iterations 1.572041 41.91467 at 40iterations 0.8809215 22.47825 at 50iterations 0.4906003 10.99998 at 60iterations 0.2723138 5.987965 at 70iterations 0.1516742 3.369276 at 80iterations 8.4275901E-02 1.776040 at 90iterations 4.6578202E-02 0.9506187 at 100iterations 2.5924835E-02 0.5820866 at 110iterations 1.4330358E-02 0.2874360 at 120iterations 7.9289991E-03 0.1650085 at 130iterations 4.3818164E-03 8.7882996E-02 at 140iterations 2.4211777E-03 5.4470062E-02 at 150iterations 1.3398397E-03 2.7972698E-02 at 160iterations 7.4239215E-04 1.5695572E-02 at 170iterations 4.1007376E-04 8.8586211E-03 at 180iterations finished qdiffx linear iterations at : 17:04:12 total time elapsed so far: 12.25000 # loops : 180 mean,max change (kT/e) : 4.1007376E-04 8.8586211E-03 energy calculations done at 12.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 17:04:14 12.383u 0.186s 0:14.07 89.2% 0+0k 0+0io 0pf+0w