Mon Oct 10 22:42:40 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 22:42:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2618 !!! WARNING: ASP 298 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6264517 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): -19.86300 31.18200 ymin,ymax (A): 19.94800 76.77600 zmin,zma (A): 9.257999 51.92600 x,y,z range (A): 51.04500 56.82800 42.66800 scale (grids/A): 0.6264517 object centre (A): 5.659500 48.36200 30.59200 number of atom coordinates read : 2618 total number of charged atoms : 2477 net assigned charge : 4.500015 assigned positive charge : 392.6977 centred at (gu) : 91.43441 88.32354 89.80611 assigned negative charge : -388.1984 centred at (gu) : 91.39878 88.59640 89.99512 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6814 nv = 96 ne = 84 npr = 53519 no. pairs analyzed = 53519 no. exposed pairs = 3047 no. arc points = 21243 no. surface atoms = 1032 nbur = 1586 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 320 mr = 3900 m= 0 mr = 28 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3000000 number of dielectric boundary points 3206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2039 ## 175 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8293 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9507366E-08 -1.0950986E-08 midg,1,midg; midg,igrid,midg 3.6360312E-08 -1.2705358E-08 1,midg,midg; igrid,midg,midg 8.4883744E-10 9.2385042E-09 gauss-seidel spectral radius is 0.9868001 estimated iterations to convergence 71 setup time was (sec) 0.5500000 now iterating at: 22:42:41 rms-change max change #iterations 0.1393305 23.08794 at 10iterations 1.3434135E-02 2.462234 at 20iterations 1.6338662E-03 0.3399391 at 30iterations 3.7014429E-04 8.4644318E-02 at 40iterations 1.0395901E-04 2.4948120E-02 at 50iterations finished qdiffx linear iterations at : 22:42:44 total time elapsed so far: 4.250000 # loops : 50 mean,max change (kT/e) : 1.0395901E-04 2.4948120E-02 energy calculations done at 4.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.430000 DelPhi exited at 22:42:45 4.438u 0.400s 0:05.27 91.6% 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 22:42:45 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 = 2618 !!! WARNING: ASP 298 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.879355 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): -19.86300 31.18200 ymin,ymax (A): 19.94800 76.77600 zmin,zma (A): 9.257999 51.92600 x,y,z range (A): 51.04500 56.82800 42.66800 scale (grids/A): 1.879355 object centre (A): 5.659500 48.36200 30.59200 number of atom coordinates read : 2618 total number of charged atoms : 2477 net assigned charge : 4.500015 assigned positive charge : 392.6977 centred at (gu) : 94.30274 84.96986 89.41776 assigned negative charge : -388.1984 centred at (gu) : 94.19610 85.78893 89.98514 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74091 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21243 grid for indexing accessible points = 1.400000 m= 25835 mr = 52595 m= 3969 mr = 19374 m= 200 mr = 2574 m= 1 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1455 time to turn everything in is 0.5900000 number of dielectric boundary points 29485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 19449 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) : 0.6264517 object centre at (A) : 5.659500 48.36200 30.59200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2253824E-02 2.8398170E-04 midg,1,midg; midg,igrid,midg 2.2651959E-02 -3.9088700E-02 1,midg,midg; igrid,midg,midg -1.0643813E-03 -3.0272566E-03 gauss-seidel spectral radius is 0.9985946 estimated iterations to convergence 211 setup time was (sec) 0.9700000 now iterating at: 22:42:46 rms-change max change #iterations 4.164100 181.7227 at 10iterations 1.918785 71.27398 at 20iterations 0.8881146 28.00018 at 30iterations 0.4104625 12.90003 at 40iterations 0.1910454 5.923489 at 50iterations 8.8924646E-02 2.796188 at 60iterations 4.1206714E-02 1.397858 at 70iterations 1.9218219E-02 0.6306152 at 80iterations 9.0071578E-03 0.2607651 at 90iterations 4.2739916E-03 0.1363449 at 100iterations 2.0800559E-03 7.2708130E-02 at 110iterations 1.0529347E-03 4.2884827E-02 at 120iterations finished qdiffx linear iterations at : 22:42:56 total time elapsed so far: 10.30000 # loops : 120 mean,max change (kT/e) : 1.0529347E-03 4.2884827E-02 energy calculations done at 10.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.46000 DelPhi exited at 22:42:56 10.465u 0.448s 0:11.38 95.7% 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 22:42:57 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 = 2618 !!! WARNING: ASP 298 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.819033 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): -19.86300 31.18200 ymin,ymax (A): 19.94800 76.77600 zmin,zma (A): 9.257999 51.92600 x,y,z range (A): 51.04500 56.82800 42.66800 scale (grids/A): 2.819033 object centre (A): 5.659500 48.36200 30.59200 number of atom coordinates read : 2618 total number of charged atoms : 2477 net assigned charge : 4.500015 assigned positive charge : 392.6977 centred at (gu) : 96.45401 82.45476 89.12659 assigned negative charge : -388.1984 centred at (gu) : 96.29404 83.68338 89.97759 start vw surface at 0.1200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 171719 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21243 grid for indexing accessible points = 1.400000 m= 85635 mr = 127243 m= 29918 mr = 71186 m= 7043 mr = 24310 m= 887 mr = 5438 m= 35 mr = 572 m= 0 mr = 15 time to grow re-entrant surface = 0.9299999 no. cavity mid-points inaccessible to solvent = 5030 time to turn everything in is 1.580000 number of dielectric boundary points 66473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 19816 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) : 1.879355 object centre at (A) : 5.659500 48.36200 30.59200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3182934 4.4912830E-02 midg,1,midg; midg,igrid,midg -0.2144724 -0.3910375 1,midg,midg; igrid,midg,midg -8.3099589E-02 -8.6046606E-02 gauss-seidel spectral radius is 0.9992414 estimated iterations to convergence 287 setup time was (sec) 1.920000 now iterating at: 22:42:59 rms-change max change #iterations 9.664620 301.8989 at 10iterations 5.565178 136.9550 at 20iterations 3.191967 70.43036 at 30iterations 1.829095 34.68156 at 40iterations 1.046832 21.21060 at 50iterations 0.5986198 11.87772 at 60iterations 0.3421214 7.184637 at 70iterations 0.1957049 3.536953 at 80iterations 0.1118999 1.959810 at 90iterations 6.3918382E-02 1.286457 at 100iterations 3.6502276E-02 0.6856079 at 110iterations 2.0911831E-02 0.4008369 at 120iterations 1.2039624E-02 0.2257679 at 130iterations 6.9596032E-03 0.1297512 at 140iterations 4.0760706E-03 8.9088440E-02 at 150iterations 2.4382717E-03 4.9335480E-02 at 160iterations 1.5138614E-03 3.7055969E-02 at 170iterations 9.8664826E-04 2.4339676E-02 at 180iterations finished qdiffx linear iterations at : 22:43:16 total time elapsed so far: 18.97000 # loops : 180 mean,max change (kT/e) : 9.8664826E-04 2.4339676E-02 energy calculations done at 18.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.14000 DelPhi exited at 22:43:17 19.141u 0.452s 0:20.10 97.4% 0+0k 0+0io 0pf+0w