Sat Oct 8 13:02:35 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 13:02:35 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2944 !!! WARNING: GLU 326 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.6400691 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): -24.90900 25.62800 ymin,ymax (A): -26.11200 25.36300 zmin,zma (A): -8.202000 47.41700 x,y,z range (A): 50.53700 51.47500 55.61900 scale (grids/A): 0.6400691 object centre (A): 0.3594999 -0.3745003 19.60750 number of atom coordinates read : 2944 total number of charged atoms : 2798 net assigned charge : 4.226040 assigned positive charge : 437.8381 centred at (gu) : 91.42205 89.96521 91.44157 assigned negative charge : -433.6130 centred at (gu) : 91.54227 89.99485 91.61800 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8177 nv = 96 ne = 84 npr = 59696 no. pairs analyzed = 59696 no. exposed pairs = 3586 no. arc points = 25161 no. surface atoms = 1207 nbur = 1737 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 441 mr = 4668 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 81 time to turn everything in is 0.3200000 number of dielectric boundary points 3897 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2469 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9781 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1509917E-08 -2.2920499E-08 midg,1,midg; midg,igrid,midg 1.0706114E-08 2.9087295E-09 1,midg,midg; igrid,midg,midg 1.6399015E-08 -1.2497157E-08 gauss-seidel spectral radius is 0.9873841 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 13:02:35 rms-change max change #iterations 0.1575088 22.23678 at 10iterations 1.6003828E-02 2.380868 at 20iterations 2.1123067E-03 0.3244896 at 30iterations 6.7499920E-04 0.1302795 at 40iterations 3.1631146E-04 6.1977386E-02 at 50iterations finished qdiffx linear iterations at : 13:02:38 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 3.1631146E-04 6.1977386E-02 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 13:02:38 3.127u 0.148s 0:03.56 91.5% 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 8 2011 at 13:02:38 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2944 !!! WARNING: GLU 326 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.920207 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): -24.90900 25.62800 ymin,ymax (A): -26.11200 25.36300 zmin,zma (A): -8.202000 47.41700 x,y,z range (A): 50.53700 51.47500 55.61900 scale (grids/A): 1.920207 object centre (A): 0.3594999 -0.3745003 19.60750 number of atom coordinates read : 2944 total number of charged atoms : 2798 net assigned charge : 4.226040 assigned positive charge : 437.8381 centred at (gu) : 94.26521 89.89471 94.32397 assigned negative charge : -433.6130 centred at (gu) : 94.62643 89.98428 94.85329 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 88228 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25161 grid for indexing accessible points = 1.400000 m= 33229 mr = 62656 m= 5349 mr = 25109 m= 303 mr = 3382 m= 4 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 4613 time to turn everything in is 0.6000000 number of dielectric boundary points 35892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 22034 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) : 0.6400691 object centre at (A) : 0.3594999 -0.3745003 19.60750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8165108E-02 2.3429086E-03 midg,1,midg; midg,igrid,midg 2.0684198E-02 1.4462572E-02 1,midg,midg; igrid,midg,midg 1.2672545E-02 -8.1972615E-04 gauss-seidel spectral radius is 0.9986884 estimated iterations to convergence 219 setup time was (sec) 0.8700000 now iterating at: 13:02:39 rms-change max change #iterations 4.589726 186.9018 at 10iterations 2.175459 77.90438 at 20iterations 1.039446 34.24063 at 30iterations 0.4922403 14.55557 at 40iterations 0.2345299 6.994432 at 50iterations 0.1114392 3.246999 at 60iterations 5.3154163E-02 1.489751 at 70iterations 2.5448095E-02 0.7412758 at 80iterations 1.2254855E-02 0.3739605 at 90iterations 6.0169385E-03 0.1835203 at 100iterations 3.1207441E-03 0.1048660 at 110iterations 1.7642035E-03 6.4890862E-02 at 120iterations finished qdiffx linear iterations at : 13:02:45 total time elapsed so far: 6.990000 # loops : 120 mean,max change (kT/e) : 1.7642035E-03 6.4890862E-02 energy calculations done at 6.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.160000 DelPhi exited at 13:02:46 7.164u 0.157s 0:07.57 96.5% 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 8 2011 at 13:02:46 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2944 !!! WARNING: GLU 326 has a net charge of -2.0000 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.880311 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): -24.90900 25.62800 ymin,ymax (A): -26.11200 25.36300 zmin,zma (A): -8.202000 47.41700 x,y,z range (A): 50.53700 51.47500 55.61900 scale (grids/A): 2.880311 object centre (A): 0.3594999 -0.3745003 19.60750 number of atom coordinates read : 2944 total number of charged atoms : 2798 net assigned charge : 4.226040 assigned positive charge : 437.8381 centred at (gu) : 96.39784 89.84184 96.48582 assigned negative charge : -433.6130 centred at (gu) : 96.93959 89.97622 97.27991 start vw surface at 0.1600000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 203679 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25161 grid for indexing accessible points = 1.400000 m= 106726 mr = 150975 m= 39955 mr = 88791 m= 9736 mr = 32595 m= 1287 mr = 7249 m= 76 mr = 775 m= 0 mr = 18 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 15148 time to turn everything in is 1.540000 number of dielectric boundary points 81056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 22372 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) : 1.920207 object centre at (A) : 0.3594999 -0.3745003 19.60750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1362426 0.1906400 midg,1,midg; midg,igrid,midg 0.2331616 0.2834172 1,midg,midg; igrid,midg,midg 4.0834885E-02 6.5163493E-02 gauss-seidel spectral radius is 0.9992788 estimated iterations to convergence 294 setup time was (sec) 1.830000 now iterating at: 13:02:48 rms-change max change #iterations 10.73347 405.5311 at 10iterations 6.313757 136.2763 at 20iterations 3.685337 74.54248 at 30iterations 2.152515 38.77624 at 40iterations 1.253108 26.63292 at 50iterations 0.7292543 12.50505 at 60iterations 0.4247353 7.152344 at 70iterations 0.2468449 4.369914 at 80iterations 0.1431518 2.447449 at 90iterations 8.3016388E-02 1.367337 at 100iterations 4.8317797E-02 0.8350353 at 110iterations 2.8066460E-02 0.5250206 at 120iterations 1.6371137E-02 0.2824116 at 130iterations 9.6316766E-03 0.1753273 at 140iterations 5.7329107E-03 0.1131363 at 150iterations 3.5295689E-03 7.1119308E-02 at 160iterations 2.2886463E-03 5.2398682E-02 at 170iterations 1.6058690E-03 3.7048340E-02 at 180iterations finished qdiffx linear iterations at : 13:02:58 total time elapsed so far: 11.50000 # loops : 180 mean,max change (kT/e) : 1.6058690E-03 3.7048340E-02 energy calculations done at 11.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.68000 DelPhi exited at 13:02:58 11.680u 0.165s 0:12.14 97.5% 0+0k 0+0io 0pf+0w