Wed Feb 15 08:54:34 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:54:35 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2843 !!! WARNING: GLU 12 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5392224 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): -26.93800 26.60100 ymin,ymax (A): 8.518000 51.12100 zmin,zma (A): -11.84900 54.17200 x,y,z range (A): 53.53900 42.60300 66.02100 scale (grids/A): 0.5392224 object centre (A): -0.1684999 29.81950 21.16150 number of atom coordinates read : 2843 total number of charged atoms : 2704 net assigned charge : 2.000007 assigned positive charge : 420.4787 centred at (gu) : 91.18899 90.61964 90.34456 assigned negative charge : -418.4794 centred at (gu) : 91.20801 90.63401 90.32413 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5302 nv = 96 ne = 84 npr = 57806 no. pairs analyzed = 57806 no. exposed pairs = 3771 no. arc points = 26515 no. surface atoms = 1256 nbur = 1587 mkacc time = 9.9999994E-02 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 = 1.568000 m= 202 mr = 2562 m= 0 mr = 7 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2738 ## 360 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7066 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0364006E-12 2.1247057E-10 midg,1,midg; midg,igrid,midg 1.4223428E-10 3.0642079E-11 1,midg,midg; igrid,midg,midg 1.4028248E-10 3.9446692E-12 gauss-seidel spectral radius is 0.9822640 estimated iterations to convergence 62 setup time was (sec) 0.4000000 now iterating at: 08:54:35 rms-change max change #iterations 6.4128689E-02 11.22164 at 10iterations 4.0393500E-03 0.7689838 at 20iterations 2.6086715E-04 4.6041489E-02 at 30iterations 1.6511329E-05 2.7265549E-03 at 40iterations 1.1107367E-06 2.3365021E-04 at 50iterations finished qdiffx linear iterations at : 08:54:38 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 1.1107367E-06 2.3365021E-04 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 08:54:39 3.541u 0.180s 0:06.30 59.0% 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 Wed Feb 15 2012 at 08:54:41 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2843 !!! WARNING: GLU 12 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.617667 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): -26.93800 26.60100 ymin,ymax (A): 8.518000 51.12100 zmin,zma (A): -11.84900 54.17200 x,y,z range (A): 53.53900 42.60300 66.02100 scale (grids/A): 1.617667 object centre (A): -0.1684999 29.81950 21.16150 number of atom coordinates read : 2843 total number of charged atoms : 2704 net assigned charge : 2.000007 assigned positive charge : 420.4787 centred at (gu) : 93.56671 91.85844 91.03311 assigned negative charge : -418.4794 centred at (gu) : 93.62379 91.90178 90.97195 start vw surface at 0.1000000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 58792 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26515 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 17155 mr = 38477 m= 1665 mr = 11145 m= 35 mr = 749 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 27276 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 342 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 20684 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) : 0.5392224 object centre at (A) : -0.1684999 29.81950 21.16150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8576479E-02 -2.1927678E-03 midg,1,midg; midg,igrid,midg -2.1777500E-03 4.7073648E-03 1,midg,midg; igrid,midg,midg 3.9618770E-03 1.0564245E-03 gauss-seidel spectral radius is 0.9981333 estimated iterations to convergence 184 setup time was (sec) 0.5200000 now iterating at: 08:54:42 rms-change max change #iterations 3.149256 184.4105 at 10iterations 1.293641 56.01361 at 20iterations 0.5330379 21.37635 at 30iterations 0.2207376 8.543093 at 40iterations 9.0805240E-02 3.363146 at 50iterations 3.7535090E-02 1.486617 at 60iterations 1.5429420E-02 0.6074402 at 70iterations 6.3709379E-03 0.2439494 at 80iterations 2.6185669E-03 9.9380493E-02 at 90iterations 1.0815511E-03 4.3426514E-02 at 100iterations 4.4752940E-04 1.7673492E-02 at 110iterations 1.8510970E-04 7.3966980E-03 at 120iterations finished qdiffx linear iterations at : 08:54:49 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 1.8510970E-04 7.3966980E-03 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.340000 DelPhi exited at 08:54:50 8.340u 0.192s 0:08.90 95.8% 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 Wed Feb 15 2012 at 08:54:54 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 ! Automatically converted by prot2crg.py # of charge parameter records: 929 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2843 !!! WARNING: GLU 12 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.426501 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): -26.93800 26.60100 ymin,ymax (A): 8.518000 51.12100 zmin,zma (A): -11.84900 54.17200 x,y,z range (A): 53.53900 42.60300 66.02100 scale (grids/A): 2.426501 object centre (A): -0.1684999 29.81950 21.16150 number of atom coordinates read : 2843 total number of charged atoms : 2704 net assigned charge : 2.000007 assigned positive charge : 420.4787 centred at (gu) : 95.34987 92.78747 91.54942 assigned negative charge : -418.4794 centred at (gu) : 95.43575 92.85271 91.45802 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 136587 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26515 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 59989 mr = 94880 m= 16174 mr = 45799 m= 2522 mr = 11635 m= 162 mr = 1539 m= 2 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 61524 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 21611 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) : 1.617667 object centre at (A) : -0.1684999 29.81950 21.16150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5220793 -0.2141389 midg,1,midg; midg,igrid,midg -5.0885286E-02 7.7283390E-02 1,midg,midg; igrid,midg,midg 7.4685685E-02 1.1731151E-02 gauss-seidel spectral radius is 0.9991229 estimated iterations to convergence 267 setup time was (sec) 0.9400000 now iterating at: 08:54:55 rms-change max change #iterations 8.290959 347.0906 at 10iterations 4.663219 183.9649 at 20iterations 2.608680 62.46755 at 30iterations 1.447396 33.70399 at 40iterations 0.8014503 20.69807 at 50iterations 0.4412475 9.963551 at 60iterations 0.2432043 6.090395 at 70iterations 0.1330955 2.809189 at 80iterations 7.3100865E-02 1.521591 at 90iterations 4.0142715E-02 0.8726196 at 100iterations 2.1987736E-02 0.4816771 at 110iterations 1.2043351E-02 0.2642093 at 120iterations 6.5793521E-03 0.1349988 at 130iterations 3.6033925E-03 8.2981110E-02 at 140iterations 1.9688895E-03 4.9388885E-02 at 150iterations 1.0742241E-03 2.3963690E-02 at 160iterations 5.8714033E-04 1.2668610E-02 at 170iterations 3.2116988E-04 7.6707304E-03 at 180iterations finished qdiffx linear iterations at : 08:55:06 total time elapsed so far: 12.06000 # loops : 180 mean,max change (kT/e) : 3.2116988E-04 7.6707304E-03 energy calculations done at 12.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 08:55:07 12.196u 0.203s 0:13.00 95.3% 0+0k 0+0io 0pf+0w