Tue Oct 11 03:17:27 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 Tue Oct 11 2011 at 03:17:28 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3402 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: HIR 298 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5348638 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): -41.03900 10.53400 ymin,ymax (A): -55.99100 3.454000 zmin,zma (A): -35.01800 31.54100 x,y,z range (A): 51.57300 59.44500 66.55901 scale (grids/A): 0.5348638 object centre (A): -15.25250 -26.26850 -1.738501 number of atom coordinates read : 3402 total number of charged atoms : 3257 net assigned charge : -8.079983 assigned positive charge : 516.4802 centred at (gu) : 90.96067 88.01755 92.35800 assigned negative charge : -524.5618 centred at (gu) : 90.88784 87.96274 92.37038 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 6408 nv = 96 ne = 84 npr = 68091 no. pairs analyzed = 68091 no. exposed pairs = 4267 no. arc points = 30391 no. surface atoms = 1419 nbur = 1983 mkacc time = 0.1500000 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= 298 mr = 3411 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3051 ## 437 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8413 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4354629E-10 -6.8003964E-10 midg,1,midg; midg,igrid,midg -9.8068220E-10 -2.8065847E-11 1,midg,midg; igrid,midg,midg -5.3989641E-10 6.9353259E-11 gauss-seidel spectral radius is 0.9820201 estimated iterations to convergence 61 setup time was (sec) 0.6200000 now iterating at: 03:17:28 rms-change max change #iterations 7.2710641E-02 12.69599 at 10iterations 4.7658170E-03 0.7532659 at 20iterations 4.1562464E-04 6.2108994E-02 at 30iterations 7.6353834E-05 1.0380983E-02 at 40iterations 1.9014840E-05 2.8119087E-03 at 50iterations finished qdiffx linear iterations at : 03:17:31 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 1.9014840E-05 2.8119087E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 03:17:32 3.420u 0.279s 0:04.09 90.2% 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 Tue Oct 11 2011 at 03:17:32 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3402 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: HIR 298 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.604591 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): -41.03900 10.53400 ymin,ymax (A): -55.99100 3.454000 zmin,zma (A): -35.01800 31.54100 x,y,z range (A): 51.57300 59.44500 66.55901 scale (grids/A): 1.604591 object centre (A): -15.25250 -26.26850 -1.738501 number of atom coordinates read : 3402 total number of charged atoms : 3257 net assigned charge : -8.079983 assigned positive charge : 516.4802 centred at (gu) : 92.88097 84.05169 97.07310 assigned negative charge : -524.5618 centred at (gu) : 92.66268 83.88778 97.11048 start vw surface at 0.2500000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 71383 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30391 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 22689 mr = 49097 m= 2263 mr = 15606 m= 54 mr = 1079 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 940 time to turn everything in is 0.6100000 number of dielectric boundary points 30600 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 441 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 24902 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) : 0.5348638 object centre at (A) : -15.25250 -26.26850 -1.738501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3332663E-02 -1.8296985E-02 midg,1,midg; midg,igrid,midg -8.1497943E-03 -2.4743663E-04 1,midg,midg; igrid,midg,midg -1.0835631E-02 -2.7400893E-03 gauss-seidel spectral radius is 0.9981577 estimated iterations to convergence 185 setup time was (sec) 0.9300000 now iterating at: 03:17:33 rms-change max change #iterations 3.524393 205.8147 at 10iterations 1.448678 57.78460 at 20iterations 0.6011382 20.65653 at 30iterations 0.2478915 8.843550 at 40iterations 0.1028372 3.499840 at 50iterations 4.2751852E-02 1.565712 at 60iterations 1.7799122E-02 0.6534042 at 70iterations 7.3751151E-03 0.2589359 at 80iterations 3.0894489E-03 0.1254938 at 90iterations 1.3056753E-03 4.3353915E-02 at 100iterations 5.6007213E-04 1.8041790E-02 at 110iterations 2.5048610E-04 8.1748962E-03 at 120iterations finished qdiffx linear iterations at : 03:17:40 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 2.5048610E-04 8.1748962E-03 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 03:17:40 7.898u 0.202s 0:08.49 95.2% 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 Tue Oct 11 2011 at 03:17:40 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3402 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: HIR 298 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.406887 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): -41.03900 10.53400 ymin,ymax (A): -55.99100 3.454000 zmin,zma (A): -35.01800 31.54100 x,y,z range (A): 51.57300 59.44500 66.55901 scale (grids/A): 2.406887 object centre (A): -15.25250 -26.26850 -1.738501 number of atom coordinates read : 3402 total number of charged atoms : 3257 net assigned charge : -8.079983 assigned positive charge : 516.4802 centred at (gu) : 94.32114 81.07742 100.6094 assigned negative charge : -524.5618 centred at (gu) : 93.99382 80.83158 100.6657 start vw surface at 0.2300000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 165961 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30391 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 78443 mr = 119823 m= 22323 mr = 62531 m= 3558 mr = 16737 m= 208 mr = 2205 m= 5 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 3158 time to turn everything in is 1.320000 number of dielectric boundary points 69133 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 24 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 26012 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) : 1.604591 object centre at (A) : -15.25250 -26.26850 -1.738501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4369390 -0.3771465 midg,1,midg; midg,igrid,midg -7.6716967E-02 2.3260549E-02 1,midg,midg; igrid,midg,midg -0.1502416 -2.6572105E-02 gauss-seidel spectral radius is 0.9991370 estimated iterations to convergence 269 setup time was (sec) 1.640000 now iterating at: 03:17:42 rms-change max change #iterations 9.178914 264.9021 at 10iterations 5.158922 129.5407 at 20iterations 2.870784 69.88986 at 30iterations 1.596420 34.37032 at 40iterations 0.8866597 18.38639 at 50iterations 0.4903267 9.778870 at 60iterations 0.2706050 5.173645 at 70iterations 0.1499513 3.226825 at 80iterations 8.2609080E-02 1.861645 at 90iterations 4.5459460E-02 0.9952726 at 100iterations 2.5082154E-02 0.4893100 at 110iterations 1.3806321E-02 0.2783952 at 120iterations 7.5914823E-03 0.1685486 at 130iterations 4.1779629E-03 8.2727432E-02 at 140iterations 2.3009072E-03 4.6175003E-02 at 150iterations 1.2699624E-03 2.4766922E-02 at 160iterations 6.9955876E-04 1.3938904E-02 at 170iterations 3.8665425E-04 8.3606839E-03 at 180iterations finished qdiffx linear iterations at : 03:17:52 total time elapsed so far: 11.57000 # loops : 180 mean,max change (kT/e) : 3.8665425E-04 8.3606839E-03 energy calculations done at 11.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.75000 DelPhi exited at 03:17:53 11.754u 0.248s 0:12.33 97.2% 0+0k 0+0io 0pf+0w