Mon Oct 10 16:05:11 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 Mon Oct 10 2011 at 16:05:11 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4905 !!! WARNING: ASP 610 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5323842 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): 7.515000 62.62100 ymin,ymax (A): 52.25200 116.5870 zmin,zma (A): -35.36200 31.50700 x,y,z range (A): 55.10600 64.33500 66.86900 scale (grids/A): 0.5323842 object centre (A): 35.06800 84.41949 -1.927502 number of atom coordinates read : 4905 total number of charged atoms : 4745 net assigned charge : 4.000031 assigned positive charge : 740.0183 centred at (gu) : 89.76771 89.95760 90.94614 assigned negative charge : -736.0231 centred at (gu) : 89.73410 89.97064 90.92122 start vw surface at 0.2200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8783 nv = 96 ne = 84 npr = 101174 no. pairs analyzed = 101174 no. exposed pairs = 5904 no. arc points = 39991 no. surface atoms = 1984 nbur = 2921 mkacc time = 0.3400000 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= 307 mr = 4798 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 4282 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4012 ## 540 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 11802 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4643616E-11 3.8793280E-10 midg,1,midg; midg,igrid,midg 2.3043234E-10 5.7140556E-11 1,midg,midg; igrid,midg,midg -8.2637279E-11 3.4089639E-10 gauss-seidel spectral radius is 0.9819542 estimated iterations to convergence 61 setup time was (sec) 1.040000 now iterating at: 16:05:13 rms-change max change #iterations 8.4742926E-02 12.90783 at 10iterations 5.8745029E-03 0.8448296 at 20iterations 1.1055348E-03 0.1960869 at 30iterations 4.1836809E-04 6.3175201E-02 at 40iterations 1.7107931E-04 2.2380829E-02 at 50iterations finished qdiffx linear iterations at : 16:05:17 total time elapsed so far: 4.900000 # loops : 50 mean,max change (kT/e) : 1.7107931E-04 2.2380829E-02 energy calculations done at 4.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.130000 DelPhi exited at 16:05:17 5.132u 0.425s 0:06.03 92.0% 0+0k 0+0io 5pf+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 Mon Oct 10 2011 at 16:05:17 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4905 !!! WARNING: ASP 610 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.597153 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): 7.515000 62.62100 ymin,ymax (A): 52.25200 116.5870 zmin,zma (A): -35.36200 31.50700 x,y,z range (A): 55.10600 64.33500 66.86900 scale (grids/A): 1.597153 object centre (A): 35.06800 84.41949 -1.927502 number of atom coordinates read : 4905 total number of charged atoms : 4745 net assigned charge : 4.000031 assigned positive charge : 740.0183 centred at (gu) : 89.30172 89.87106 92.83701 assigned negative charge : -736.0231 centred at (gu) : 89.20174 89.91144 92.76334 start vw surface at 0.2200000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 99326 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39991 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 30601 mr = 70680 m= 2940 mr = 20984 m= 73 mr = 1424 m= 0 mr = 3 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 1239 time to turn everything in is 1.010000 number of dielectric boundary points 39849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 489 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 36092 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) : 0.5323842 object centre at (A) : 35.06800 84.41949 -1.927502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5308475E-02 9.6056499E-03 midg,1,midg; midg,igrid,midg 7.2775846E-03 1.2901434E-02 1,midg,midg; igrid,midg,midg 1.2098151E-03 7.0836111E-03 gauss-seidel spectral radius is 0.9982868 estimated iterations to convergence 192 setup time was (sec) 1.420000 now iterating at: 16:05:19 rms-change max change #iterations 4.213228 181.0804 at 10iterations 1.794963 52.18449 at 20iterations 0.7699193 24.53804 at 30iterations 0.3294744 9.973841 at 40iterations 0.1410187 4.271530 at 50iterations 6.0428143E-02 1.900333 at 60iterations 2.6070807E-02 0.7682190 at 70iterations 1.1253675E-02 0.3680267 at 80iterations 4.9436879E-03 0.1475449 at 90iterations 2.2514688E-03 6.8335533E-02 at 100iterations 1.0912035E-03 3.5873413E-02 at 110iterations 6.0183660E-04 1.8428802E-02 at 120iterations finished qdiffx linear iterations at : 16:05:29 total time elapsed so far: 11.43000 # loops : 120 mean,max change (kT/e) : 6.0183660E-04 1.8428802E-02 energy calculations done at 11.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.64000 DelPhi exited at 16:05:30 11.644u 0.529s 0:12.77 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 Mon Oct 10 2011 at 16:05:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4905 !!! WARNING: ASP 610 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.395729 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): 7.515000 62.62100 ymin,ymax (A): 52.25200 116.5870 zmin,zma (A): -35.36200 31.50700 x,y,z range (A): 55.10600 64.33500 66.86900 scale (grids/A): 2.395729 object centre (A): 35.06800 84.41949 -1.927502 number of atom coordinates read : 4905 total number of charged atoms : 4745 net assigned charge : 4.000031 assigned positive charge : 740.0183 centred at (gu) : 88.95213 89.80621 94.25503 assigned negative charge : -736.0231 centred at (gu) : 88.80250 89.86697 94.14491 start vw surface at 0.2300000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 231753 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39991 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 107623 mr = 173233 m= 29387 mr = 85425 m= 4553 mr = 22015 m= 307 mr = 2924 m= 5 mr = 139 m= 0 mr = 0 time to grow re-entrant surface = 1.540000 no. cavity mid-points inaccessible to solvent = 4644 time to turn everything in is 2.500000 number of dielectric boundary points 89892 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 2.680000 number of grid points assigned charge 37889 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) : 1.597153 object centre at (A) : 35.06800 84.41949 -1.927502 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3107060 0.2974378 midg,1,midg; midg,igrid,midg 4.9995225E-02 0.2525229 1,midg,midg; igrid,midg,midg 3.8708378E-02 0.1136040 gauss-seidel spectral radius is 0.9992136 estimated iterations to convergence 282 setup time was (sec) 2.900000 now iterating at: 16:05:34 rms-change max change #iterations 11.04827 333.7356 at 10iterations 6.463094 142.6066 at 20iterations 3.757642 88.51678 at 30iterations 2.170822 48.85627 at 40iterations 1.248100 26.27939 at 50iterations 0.7152535 13.38314 at 60iterations 0.4087606 8.558268 at 70iterations 0.2338069 4.298622 at 80iterations 0.1330850 2.369919 at 90iterations 7.5812429E-02 1.343399 at 100iterations 4.3154269E-02 0.7623844 at 110iterations 2.4547739E-02 0.5000815 at 120iterations 1.3999635E-02 0.2446747 at 130iterations 8.0041224E-03 0.1376362 at 140iterations 4.6166223E-03 8.1848145E-02 at 150iterations 2.6979723E-03 4.7555923E-02 at 160iterations 1.6227991E-03 3.0517578E-02 at 170iterations 1.0219024E-03 1.7528534E-02 at 180iterations finished qdiffx linear iterations at : 16:05:51 total time elapsed so far: 20.14000 # loops : 180 mean,max change (kT/e) : 1.0219024E-03 1.7528534E-02 energy calculations done at 20.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.36000 DelPhi exited at 16:05:52 20.369u 0.532s 0:21.25 98.3% 0+0k 0+0io 0pf+0w