Tue Oct 11 06:43:47 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 06:43:47 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7108341 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): -19.66000 24.78500 ymin,ymax (A): -13.01900 28.00800 zmin,zma (A): -3.560000 46.52200 x,y,z range (A): 44.44500 41.02700 50.08200 scale (grids/A): 0.7108341 object centre (A): 2.562500 7.494501 21.48100 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 319.5760 centred at (gu) : 89.74050 90.10035 90.62631 assigned negative charge : -313.6311 centred at (gu) : 89.60593 90.11356 90.69283 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6843 nv = 96 ne = 84 npr = 43719 no. pairs analyzed = 43719 no. exposed pairs = 2351 no. arc points = 16048 no. surface atoms = 803 nbur = 1286 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 383 mr = 3960 m= 1 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.2900000 number of dielectric boundary points 3214 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1494 ## 141 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7828 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.0092690E-08 2.1038167E-08 midg,1,midg; midg,igrid,midg 6.0767825E-08 4.8668504E-08 1,midg,midg; igrid,midg,midg -1.9378044E-08 1.1984800E-07 gauss-seidel spectral radius is 0.9896756 estimated iterations to convergence 80 setup time was (sec) 0.5300000 now iterating at: 06:43:47 rms-change max change #iterations 0.2105822 28.44450 at 10iterations 2.6187057E-02 3.588353 at 20iterations 3.2755742E-03 0.4078350 at 30iterations 4.1872667E-04 5.9594154E-02 at 40iterations 5.6617981E-05 9.9258423E-03 at 50iterations finished qdiffx linear iterations at : 06:43:50 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 5.6617981E-05 9.9258423E-03 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 06:43:50 3.309u 0.149s 0:03.74 91.9% 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 06:43:50 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.132503 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): -19.66000 24.78500 ymin,ymax (A): -13.01900 28.00800 zmin,zma (A): -3.560000 46.52200 x,y,z range (A): 44.44500 41.02700 50.08200 scale (grids/A): 2.132503 object centre (A): 2.562500 7.494501 21.48100 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 319.5760 centred at (gu) : 89.22163 90.30116 91.87894 assigned negative charge : -313.6311 centred at (gu) : 88.81805 90.34091 92.07860 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 72851 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16048 grid for indexing accessible points = 1.400000 m= 26893 mr = 52243 m= 4838 mr = 20003 m= 453 mr = 3111 m= 16 mr = 237 m= 0 mr = 6 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2614 time to turn everything in is 0.5600000 number of dielectric boundary points 29451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 15529 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) : 0.7108341 object centre at (A) : 2.562500 7.494501 21.48100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4003259E-02 6.4134315E-02 midg,1,midg; midg,igrid,midg 2.3790045E-02 5.4395506E-03 1,midg,midg; igrid,midg,midg 1.1145543E-02 3.5675466E-02 gauss-seidel spectral radius is 0.9988322 estimated iterations to convergence 232 setup time was (sec) 0.8400000 now iterating at: 06:43:51 rms-change max change #iterations 4.685902 170.5434 at 10iterations 2.320536 81.10992 at 20iterations 1.146890 37.77193 at 30iterations 0.5723758 16.57841 at 40iterations 0.2833338 8.513388 at 50iterations 0.1407884 4.235117 at 60iterations 6.9938786E-02 2.186035 at 70iterations 3.4712888E-02 1.098303 at 80iterations 1.7238433E-02 0.4897757 at 90iterations 8.5556069E-03 0.2959185 at 100iterations 4.2473893E-03 0.1215448 at 110iterations 2.1188138E-03 6.6055298E-02 at 120iterations finished qdiffx linear iterations at : 06:43:58 total time elapsed so far: 7.210000 # loops : 120 mean,max change (kT/e) : 2.1188138E-03 6.6055298E-02 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.400000 DelPhi exited at 06:43:59 7.400u 0.170s 0:08.11 93.3% 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 Tue Oct 11 2011 at 06:43:59 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2089 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.198754 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): -19.66000 24.78500 ymin,ymax (A): -13.01900 28.00800 zmin,zma (A): -3.560000 46.52200 x,y,z range (A): 44.44500 41.02700 50.08200 scale (grids/A): 3.198754 object centre (A): 2.562500 7.494501 21.48100 number of atom coordinates read : 2089 total number of charged atoms : 1955 net assigned charge : 5.945010 assigned positive charge : 319.5760 centred at (gu) : 88.83235 90.45174 92.81829 assigned negative charge : -313.6311 centred at (gu) : 88.22704 90.51138 93.11787 start vw surface at 0.1500000 fill in re-entrant regions at 0.8500000 boundary points on vw surface= 168766 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16048 grid for indexing accessible points = 1.400000 m= 86577 mr = 126411 m= 32667 mr = 71633 m= 9069 mr = 26420 m= 1795 mr = 6825 m= 197 mr = 1301 m= 10 mr = 120 m= 0 mr = 7 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 8489 time to turn everything in is 1.790000 number of dielectric boundary points 66364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 15640 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) : 2.132503 object centre at (A) : 2.562500 7.494501 21.48100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2880128 0.6681848 midg,1,midg; midg,igrid,midg 0.1927806 2.0997480E-02 1,midg,midg; igrid,midg,midg 0.2542166 0.3439435 gauss-seidel spectral radius is 0.9992895 estimated iterations to convergence 296 setup time was (sec) 2.080000 now iterating at: 06:44:01 rms-change max change #iterations 10.32862 387.0842 at 10iterations 6.098405 162.1584 at 20iterations 3.588165 95.53026 at 30iterations 2.111035 46.24020 at 40iterations 1.236577 22.96908 at 50iterations 0.7234605 13.24362 at 60iterations 0.4238653 7.926722 at 70iterations 0.2476516 4.672440 at 80iterations 0.1444929 2.930396 at 90iterations 8.4344611E-02 1.500200 at 100iterations 4.9241912E-02 0.8299332 at 110iterations 2.8780879E-02 0.4661713 at 120iterations 1.6866388E-02 0.3116398 at 130iterations 9.8711411E-03 0.1804504 at 140iterations 5.8159544E-03 9.4901085E-02 at 150iterations 3.4439361E-03 6.7058563E-02 at 160iterations 2.0705278E-03 3.8154602E-02 at 170iterations 1.2712657E-03 2.4070740E-02 at 180iterations finished qdiffx linear iterations at : 06:44:11 total time elapsed so far: 12.14000 # loops : 180 mean,max change (kT/e) : 1.2712657E-03 2.4070740E-02 energy calculations done at 12.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.33000 DelPhi exited at 06:44:12 12.335u 0.175s 0:12.91 96.8% 0+0k 0+0io 0pf+0w