Sat Oct 15 15:03:39 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 15:03:39 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2666 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 0.6665668 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): -21.53600 24.94500 ymin,ymax (A): 10.83100 64.23900 zmin,zma (A): -17.69600 30.20900 x,y,z range (A): 46.48100 53.40800 47.90500 scale (grids/A): 0.6665668 object centre (A): 1.704500 37.53500 6.256500 number of atom coordinates read : 2666 total number of charged atoms : 2531 net assigned charge : 3.000015 assigned positive charge : 409.6965 centred at (gu) : 89.23032 89.86500 90.34018 assigned negative charge : -406.6974 centred at (gu) : 89.38519 89.58959 90.39066 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7947 nv = 96 ne = 84 npr = 54787 no. pairs analyzed = 54787 no. exposed pairs = 3293 no. arc points = 22429 no. surface atoms = 1105 nbur = 1561 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 482 mr = 4559 m= 3 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 72 time to turn everything in is 0.2000000 number of dielectric boundary points 3826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2107 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 9329 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9909086E-08 -3.6702916E-09 midg,1,midg; midg,igrid,midg -6.2152452E-08 7.2506552E-08 1,midg,midg; igrid,midg,midg 5.4460298E-08 -2.5031294E-08 gauss-seidel spectral radius is 0.9883380 estimated iterations to convergence 76 setup time was (sec) 0.3900000 now iterating at: 15:03:40 rms-change max change #iterations 0.1801780 22.81964 at 10iterations 2.0241460E-02 2.659462 at 20iterations 3.0325274E-03 0.6043091 at 30iterations 8.3723752E-04 0.1829071 at 40iterations 2.9254306E-04 6.5734863E-02 at 50iterations finished qdiffx linear iterations at : 15:03:43 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.9254306E-04 6.5734863E-02 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 15:03:43 3.390u 0.198s 0:03.94 90.8% 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 Sat Oct 15 2011 at 15:03:43 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2666 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 1.999701 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): -21.53600 24.94500 ymin,ymax (A): 10.83100 64.23900 zmin,zma (A): -17.69600 30.20900 x,y,z range (A): 46.48100 53.40800 47.90500 scale (grids/A): 1.999701 object centre (A): 1.704500 37.53500 6.256500 number of atom coordinates read : 2666 total number of charged atoms : 2531 net assigned charge : 3.000015 assigned positive charge : 409.6965 centred at (gu) : 87.69025 89.59423 91.02011 assigned negative charge : -406.6974 centred at (gu) : 88.15521 88.76841 91.17155 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 85760 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22429 grid for indexing accessible points = 1.400000 m= 32202 mr = 60788 m= 5373 mr = 24114 m= 373 mr = 3532 m= 7 mr = 157 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2834 time to turn everything in is 0.4400000 number of dielectric boundary points 35124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 120 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20030 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) : 0.6665668 object centre at (A) : 1.704500 37.53500 6.256500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4358443E-02 -2.3262011E-02 midg,1,midg; midg,igrid,midg -6.7434490E-02 7.0188165E-02 1,midg,midg; igrid,midg,midg 5.5078108E-02 -1.5816411E-02 gauss-seidel spectral radius is 0.9987644 estimated iterations to convergence 225 setup time was (sec) 0.6700000 now iterating at: 15:03:44 rms-change max change #iterations 4.813177 182.4867 at 10iterations 2.342498 80.28525 at 20iterations 1.135713 35.06718 at 30iterations 0.5520251 16.19663 at 40iterations 0.2684967 8.172120 at 50iterations 0.1301526 3.603500 at 60iterations 6.3729569E-02 1.986095 at 70iterations 3.1200388E-02 0.8823700 at 80iterations 1.5426889E-02 0.4502220 at 90iterations 7.7932919E-03 0.2425690 at 100iterations 4.0692263E-03 0.1446457 at 110iterations 2.2549832E-03 9.1796875E-02 at 120iterations finished qdiffx linear iterations at : 15:03:52 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 2.2549832E-03 9.1796875E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 15:03:52 8.066u 0.309s 0:09.03 92.5% 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 15:03:52 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2666 !!! WARNING: FMN 398 has a net charge of -2.0000 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: 2.999551 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): -21.53600 24.94500 ymin,ymax (A): 10.83100 64.23900 zmin,zma (A): -17.69600 30.20900 x,y,z range (A): 46.48100 53.40800 47.90500 scale (grids/A): 2.999551 object centre (A): 1.704500 37.53500 6.256500 number of atom coordinates read : 2666 total number of charged atoms : 2531 net assigned charge : 3.000015 assigned positive charge : 409.6965 centred at (gu) : 86.53522 89.39123 91.52985 assigned negative charge : -406.6974 centred at (gu) : 87.23271 88.15261 91.75717 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 198249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22429 grid for indexing accessible points = 1.400000 m= 102631 mr = 146493 m= 38721 mr = 84866 m= 9834 mr = 31727 m= 1616 mr = 7551 m= 129 mr = 1160 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 9499 time to turn everything in is 1.100000 number of dielectric boundary points 79317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 20247 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) : 1.999701 object centre at (A) : 1.704500 37.53500 6.256500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1963241 -0.2553607 midg,1,midg; midg,igrid,midg -0.7749487 0.9325063 1,midg,midg; igrid,midg,midg 0.4333213 -0.1752947 gauss-seidel spectral radius is 0.9992890 estimated iterations to convergence 296 setup time was (sec) 1.350000 now iterating at: 15:03:54 rms-change max change #iterations 11.04027 399.7745 at 10iterations 6.494777 146.3027 at 20iterations 3.816995 80.30195 at 30iterations 2.237854 46.81810 at 40iterations 1.308980 25.25463 at 50iterations 0.7655742 14.51454 at 60iterations 0.4471829 8.200424 at 70iterations 0.2607310 4.444324 at 80iterations 0.1522086 2.577000 at 90iterations 8.8720776E-02 1.535847 at 100iterations 5.1741611E-02 0.9750085 at 110iterations 3.0258575E-02 0.5634232 at 120iterations 1.7755946E-02 0.3327522 at 130iterations 1.0514300E-02 0.2072830 at 140iterations 6.3345502E-03 0.1277008 at 150iterations 3.9214534E-03 8.2363129E-02 at 160iterations 2.5486092E-03 5.8464050E-02 at 170iterations 1.7619791E-03 4.5116425E-02 at 180iterations finished qdiffx linear iterations at : 15:04:07 total time elapsed so far: 13.50000 # loops : 180 mean,max change (kT/e) : 1.7619791E-03 4.5116425E-02 energy calculations done at 13.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.63000 DelPhi exited at 15:04:07 13.632u 0.297s 0:14.79 94.1% 0+0k 0+0io 0pf+0w