Mon Oct 10 14:00:24 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 Mon Oct 10 2011 at 14:00:24 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3364 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5744345 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): -11.17000 50.80400 ymin,ymax (A): -12.56700 42.37700 zmin,zma (A): 19.55200 75.74200 x,y,z range (A): 61.97400 54.94400 56.19000 scale (grids/A): 0.5744345 object centre (A): 19.81700 14.90500 47.64700 number of atom coordinates read : 3364 total number of charged atoms : 3207 net assigned charge : 5.030016 assigned positive charge : 521.5959 centred at (gu) : 90.90565 89.95171 87.76965 assigned negative charge : -516.5671 centred at (gu) : 90.82410 90.01172 87.76939 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7432 nv = 96 ne = 84 npr = 65270 no. pairs analyzed = 65270 no. exposed pairs = 4485 no. arc points = 32061 no. surface atoms = 1508 nbur = 1856 mkacc time = 0.1800000 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 = 1.484000 m= 378 mr = 3691 m= 1 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 4087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3144 ## 347 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 9314 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4670515E-09 5.3584920E-10 midg,1,midg; midg,igrid,midg 2.1620614E-09 -3.8899980E-10 1,midg,midg; igrid,midg,midg -6.8163791E-10 3.2048491E-09 gauss-seidel spectral radius is 0.9843987 estimated iterations to convergence 66 setup time was (sec) 0.7800000 now iterating at: 14:00:25 rms-change max change #iterations 9.8805338E-02 15.80354 at 10iterations 7.6004211E-03 1.308338 at 20iterations 5.8680517E-04 9.0995789E-02 at 30iterations 6.8110014E-05 1.0910034E-02 at 40iterations 2.7478101E-05 3.8056374E-03 at 50iterations finished qdiffx linear iterations at : 14:00:29 total time elapsed so far: 4.690000 # loops : 50 mean,max change (kT/e) : 2.7478101E-05 3.8056374E-03 energy calculations done at 4.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.870000 DelPhi exited at 14:00:30 4.879u 0.341s 0:06.31 82.5% 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 14:00:30 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3364 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.723303 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): -11.17000 50.80400 ymin,ymax (A): -12.56700 42.37700 zmin,zma (A): 19.55200 75.74200 x,y,z range (A): 61.97400 54.94400 56.19000 scale (grids/A): 1.723303 object centre (A): 19.81700 14.90500 47.64700 number of atom coordinates read : 3364 total number of charged atoms : 3207 net assigned charge : 5.030016 assigned positive charge : 521.5959 centred at (gu) : 92.71622 89.85425 83.30849 assigned negative charge : -516.5671 centred at (gu) : 92.47215 90.03487 83.30785 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 81037 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32061 grid for indexing accessible points = 1.400000 m= 27028 mr = 53986 m= 3496 mr = 18189 m= 159 mr = 1761 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7400000 number of dielectric boundary points 37750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 276 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 24846 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) : 0.5744345 object centre at (A) : 19.81700 14.90500 47.64700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7353697E-02 6.1672037E-03 midg,1,midg; midg,igrid,midg 2.2473790E-02 -5.8754911E-03 1,midg,midg; igrid,midg,midg -6.0545150E-03 -6.7669908E-03 gauss-seidel spectral radius is 0.9984213 estimated iterations to convergence 200 setup time was (sec) 1.120000 now iterating at: 14:00:32 rms-change max change #iterations 4.100719 180.4083 at 10iterations 1.813815 66.29560 at 20iterations 0.8027209 27.98830 at 30iterations 0.3551939 11.41489 at 40iterations 0.1576097 5.172889 at 50iterations 7.0280321E-02 2.541248 at 60iterations 3.1109659E-02 0.9656227 at 70iterations 1.3878847E-02 0.4370613 at 80iterations 6.1340723E-03 0.2228699 at 90iterations 2.7205385E-03 9.6385956E-02 at 100iterations 1.2169364E-03 3.6273479E-02 at 110iterations 5.4574903E-04 1.8127441E-02 at 120iterations finished qdiffx linear iterations at : 14:00:41 total time elapsed so far: 10.90000 # loops : 120 mean,max change (kT/e) : 5.4574903E-04 1.8127441E-02 energy calculations done at 10.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.08000 DelPhi exited at 14:00:43 11.087u 0.445s 0:13.01 88.5% 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 14:00:44 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: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3364 !!! WARNING: LLP 1 has a net charge of 1.3200 !!! WARNING: LLP 2 has a net charge of 0.2100 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: 2.584955 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): -11.17000 50.80400 ymin,ymax (A): -12.56700 42.37700 zmin,zma (A): 19.55200 75.74200 x,y,z range (A): 61.97400 54.94400 56.19000 scale (grids/A): 2.584955 object centre (A): 19.81700 14.90500 47.64700 number of atom coordinates read : 3364 total number of charged atoms : 3207 net assigned charge : 5.030016 assigned positive charge : 521.5959 centred at (gu) : 94.07427 89.78133 79.96241 assigned negative charge : -516.5671 centred at (gu) : 93.70802 90.05224 79.96167 start vw surface at 0.1900000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 188067 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32061 grid for indexing accessible points = 1.400000 m= 89810 mr = 132712 m= 28849 mr = 69795 m= 5748 mr = 21346 m= 597 mr = 3763 m= 25 mr = 304 m= 0 mr = 8 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.690000 number of dielectric boundary points 85168 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 25629 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) : 1.723303 object centre at (A) : 19.81700 14.90500 47.64700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2940042 7.6078422E-02 midg,1,midg; midg,igrid,midg 0.3523065 -7.8430995E-02 1,midg,midg; igrid,midg,midg 9.4998471E-02 -0.5484421 gauss-seidel spectral radius is 0.9992256 estimated iterations to convergence 284 setup time was (sec) 2.090000 now iterating at: 14:00:46 rms-change max change #iterations 10.55867 307.4050 at 10iterations 6.242734 172.0699 at 20iterations 3.652970 95.85834 at 30iterations 2.118023 59.04446 at 40iterations 1.222145 27.35603 at 50iterations 0.7017966 14.79290 at 60iterations 0.4035931 8.826036 at 70iterations 0.2307066 4.597254 at 80iterations 0.1321812 2.661183 at 90iterations 7.5428553E-02 1.568766 at 100iterations 4.2999517E-02 0.8606684 at 110iterations 2.4486588E-02 0.4830704 at 120iterations 1.3958479E-02 0.2894430 at 130iterations 7.9519004E-03 0.1684303 at 140iterations 4.5326971E-03 8.8378906E-02 at 150iterations 2.5878740E-03 4.7718763E-02 at 160iterations 1.4846956E-03 2.8619051E-02 at 170iterations 8.6698361E-04 1.6483784E-02 at 180iterations finished qdiffx linear iterations at : 14:01:02 total time elapsed so far: 17.47000 # loops : 180 mean,max change (kT/e) : 8.6698361E-04 1.6483784E-02 energy calculations done at 17.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.64000 DelPhi exited at 14:01:03 17.642u 0.359s 0:19.04 94.4% 0+0k 0+0io 0pf+0w