Sat Oct 8 16:21:12 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 Sat Oct 8 2011 at 16:21:12 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2355 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 0.5854493 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): -2.314000 46.37400 ymin,ymax (A): -15.82600 29.60300 zmin,zma (A): -19.10100 41.70700 x,y,z range (A): 48.68800 45.42900 60.80800 scale (grids/A): 0.5854493 object centre (A): 22.03000 6.888500 11.30300 number of atom coordinates read : 2355 total number of charged atoms : 2262 net assigned charge : 3.806002 assigned positive charge : 349.2821 centred at (gu) : 90.29200 88.83463 88.76495 assigned negative charge : -345.4768 centred at (gu) : 90.33875 88.95957 88.80000 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5244 nv = 96 ne = 84 npr = 48440 no. pairs analyzed = 48440 no. exposed pairs = 2942 no. arc points = 20369 no. surface atoms = 1004 nbur = 1351 mkacc time = 0.1200000 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 = 1.456000 m= 207 mr = 2760 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2679 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2109 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6747 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2280824E-09 1.9341924E-10 midg,1,midg; midg,igrid,midg 4.5682658E-09 -1.2260772E-09 1,midg,midg; igrid,midg,midg 1.7872193E-09 -6.3228920E-13 gauss-seidel spectral radius is 0.9848846 estimated iterations to convergence 67 setup time was (sec) 0.5800000 now iterating at: 16:21:13 rms-change max change #iterations 9.0128317E-02 20.06926 at 10iterations 7.1141408E-03 1.107476 at 20iterations 5.9059414E-04 9.3902588E-02 at 30iterations 6.2125568E-05 1.2088776E-02 at 40iterations 1.1371218E-05 2.4800301E-03 at 50iterations finished qdiffx linear iterations at : 16:21:17 total time elapsed so far: 4.560000 # loops : 50 mean,max change (kT/e) : 1.1371218E-05 2.4800301E-03 energy calculations done at 4.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.720000 DelPhi exited at 16:21:17 4.728u 0.385s 0:05.42 94.0% 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 Sat Oct 8 2011 at 16:21:17 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2355 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 1.756348 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): -2.314000 46.37400 ymin,ymax (A): -15.82600 29.60300 zmin,zma (A): -19.10100 41.70700 x,y,z range (A): 48.68800 45.42900 60.80800 scale (grids/A): 1.756348 object centre (A): 22.03000 6.888500 11.30300 number of atom coordinates read : 2355 total number of charged atoms : 2262 net assigned charge : 3.806002 assigned positive charge : 349.2821 centred at (gu) : 90.87571 86.50361 86.29424 assigned negative charge : -345.4768 centred at (gu) : 91.01612 86.87875 86.39985 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 57497 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20369 grid for indexing accessible points = 1.400000 m= 18495 mr = 39301 m= 2341 mr = 13064 m= 81 mr = 1369 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 24670 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 17602 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) : 0.5854493 object centre at (A) : 22.03000 6.888500 11.30300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7457716E-02 1.3504710E-02 midg,1,midg; midg,igrid,midg 1.2885057E-02 -2.2273182E-03 1,midg,midg; igrid,midg,midg 5.0321389E-03 -1.6812766E-02 gauss-seidel spectral radius is 0.9983679 estimated iterations to convergence 196 setup time was (sec) 0.7800000 now iterating at: 16:21:18 rms-change max change #iterations 3.392172 174.4995 at 10iterations 1.485293 55.76892 at 20iterations 0.6488771 25.71268 at 30iterations 0.2838813 10.63921 at 40iterations 0.1241647 4.624851 at 50iterations 5.4155264E-02 1.887780 at 60iterations 2.3585826E-02 0.8277740 at 70iterations 1.0320447E-02 0.3673458 at 80iterations 4.5198388E-03 0.1881542 at 90iterations 1.9766744E-03 7.5048447E-02 at 100iterations 8.6440798E-04 3.0322075E-02 at 110iterations 3.7783803E-04 1.3229370E-02 at 120iterations finished qdiffx linear iterations at : 16:21:28 total time elapsed so far: 10.39000 # loops : 120 mean,max change (kT/e) : 3.7783803E-04 1.3229370E-02 energy calculations done at 10.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.55000 DelPhi exited at 16:21:28 10.552u 0.427s 0:11.27 97.3% 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 8 2011 at 16:21:28 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2355 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 has a net charge of -0.0940 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: 2.634522 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): -2.314000 46.37400 ymin,ymax (A): -15.82600 29.60300 zmin,zma (A): -19.10100 41.70700 x,y,z range (A): 48.68800 45.42900 60.80800 scale (grids/A): 2.634522 object centre (A): 22.03000 6.888500 11.30300 number of atom coordinates read : 2355 total number of charged atoms : 2262 net assigned charge : 3.806002 assigned positive charge : 349.2821 centred at (gu) : 91.31358 84.75517 84.44125 assigned negative charge : -345.4768 centred at (gu) : 91.52414 85.31804 84.59975 start vw surface at 0.1100000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 133453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20369 grid for indexing accessible points = 1.400000 m= 62069 mr = 95841 m= 19766 mr = 49531 m= 3951 mr = 15531 m= 313 mr = 2864 m= 11 mr = 167 m= 0 mr = 3 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 55626 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 18091 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) : 1.756348 object centre at (A) : 22.03000 6.888500 11.30300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1923652 0.4489866 midg,1,midg; midg,igrid,midg 0.1381374 -3.6926281E-02 1,midg,midg; igrid,midg,midg 7.1394868E-02 -0.2859195 gauss-seidel spectral radius is 0.9991791 estimated iterations to convergence 276 setup time was (sec) 1.510000 now iterating at: 16:21:30 rms-change max change #iterations 8.374211 301.4972 at 10iterations 4.773155 120.5881 at 20iterations 2.701526 71.38873 at 30iterations 1.525852 33.43130 at 40iterations 0.8593798 20.30999 at 50iterations 0.4831932 10.28129 at 60iterations 0.2716577 6.685499 at 70iterations 0.1522861 3.330200 at 80iterations 8.5001394E-02 1.944473 at 90iterations 4.7546312E-02 1.047058 at 100iterations 2.6675479E-02 0.5473328 at 110iterations 1.4879290E-02 0.3071370 at 120iterations 8.3251297E-03 0.1735840 at 130iterations 4.6383492E-03 9.2992306E-02 at 140iterations 2.5989432E-03 5.4168701E-02 at 150iterations 1.4592670E-03 3.0162811E-02 at 160iterations 8.1642164E-04 1.7978668E-02 at 170iterations 4.6093820E-04 1.1594772E-02 at 180iterations finished qdiffx linear iterations at : 16:21:47 total time elapsed so far: 18.49000 # loops : 180 mean,max change (kT/e) : 4.6093820E-04 1.1594772E-02 energy calculations done at 18.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.66000 DelPhi exited at 16:21:48 18.665u 0.459s 0:19.43 98.3% 0+0k 0+0io 0pf+0w