Sat Oct 15 14:44:40 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 Sat Oct 15 2011 at 14:44:41 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3013 !!! WARNING: SER 32 has a net charge of 0.5000 !!! WARNING: LYS 121 has a net charge of 1.5000 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: 0.5479789 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): -17.30500 47.66100 ymin,ymax (A): -28.30300 17.62300 zmin,zma (A): -43.40700 4.877000 x,y,z range (A): 64.96600 45.92600 48.28400 scale (grids/A): 0.5479789 object centre (A): 15.17800 -5.340000 -19.26500 number of atom coordinates read : 3013 total number of charged atoms : 2872 net assigned charge : -1.499979 assigned positive charge : 451.4549 centred at (gu) : 89.38724 90.02611 89.73284 assigned negative charge : -452.9561 centred at (gu) : 89.33215 89.90786 89.62368 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5816 nv = 96 ne = 84 npr = 60503 no. pairs analyzed = 60503 no. exposed pairs = 3895 no. arc points = 27582 no. surface atoms = 1316 nbur = 1697 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 = 1.596000 m= 223 mr = 2889 m= 0 mr = 4 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2881 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7726 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.6487152E-10 6.4567740E-10 midg,1,midg; midg,igrid,midg -9.6438091E-10 7.6010909E-10 1,midg,midg; igrid,midg,midg -5.8228550E-10 2.6033536E-10 gauss-seidel spectral radius is 0.9828365 estimated iterations to convergence 63 setup time was (sec) 0.4500000 now iterating at: 14:44:42 rms-change max change #iterations 7.4413016E-02 12.57295 at 10iterations 4.9980907E-03 0.7774696 at 20iterations 3.2746440E-04 6.4205170E-02 at 30iterations 2.2309299E-05 3.5972595E-03 at 40iterations 1.5379757E-06 2.6702881E-04 at 50iterations finished qdiffx linear iterations at : 14:44:47 total time elapsed so far: 3.480000 # loops : 50 mean,max change (kT/e) : 1.5379757E-06 2.6702881E-04 energy calculations done at 3.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 14:44:48 3.617u 0.199s 0:06.65 57.1% 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 Sat Oct 15 2011 at 14:44:48 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 = 3013 !!! WARNING: SER 32 has a net charge of 0.5000 !!! WARNING: LYS 121 has a net charge of 1.5000 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: 1.643937 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): -17.30500 47.66100 ymin,ymax (A): -28.30300 17.62300 zmin,zma (A): -43.40700 4.877000 x,y,z range (A): 64.96600 45.92600 48.28400 scale (grids/A): 1.643937 object centre (A): 15.17800 -5.340000 -19.26500 number of atom coordinates read : 3013 total number of charged atoms : 2872 net assigned charge : -1.499979 assigned positive charge : 451.4549 centred at (gu) : 88.16062 90.07761 89.19743 assigned negative charge : -452.9561 centred at (gu) : 87.99615 89.72321 88.87085 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65122 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27582 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19113 mr = 43215 m= 1836 mr = 12775 m= 51 mr = 800 m= 0 mr = 1 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 658 time to turn everything in is 0.3200000 number of dielectric boundary points 29331 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 355 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 22042 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) : 0.5479789 object centre at (A) : 15.17800 -5.340000 -19.26500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7592100E-02 5.3817709E-03 midg,1,midg; midg,igrid,midg -3.1679962E-03 5.0996663E-03 1,midg,midg; igrid,midg,midg -2.0792136E-02 7.1767075E-03 gauss-seidel spectral radius is 0.9982172 estimated iterations to convergence 188 setup time was (sec) 0.5300000 now iterating at: 14:44:49 rms-change max change #iterations 3.393226 163.7504 at 10iterations 1.422756 54.32431 at 20iterations 0.5964070 21.29303 at 30iterations 0.2502759 8.768627 at 40iterations 0.1047278 3.904670 at 50iterations 4.4092901E-02 1.600490 at 60iterations 1.8542390E-02 0.6442032 at 70iterations 7.7707740E-03 0.2616673 at 80iterations 3.2607564E-03 0.1255064 at 90iterations 1.3706749E-03 4.9346924E-02 at 100iterations 5.7489617E-04 2.2262573E-02 at 110iterations 2.4148679E-04 8.7871552E-03 at 120iterations finished qdiffx linear iterations at : 14:45:07 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 2.4148679E-04 8.7871552E-03 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 14:45:07 7.946u 0.231s 0:19.45 42.0% 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 Sat Oct 15 2011 at 14:45:07 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 = 3013 !!! WARNING: SER 32 has a net charge of 0.5000 !!! WARNING: LYS 121 has a net charge of 1.5000 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: 2.465905 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): -17.30500 47.66100 ymin,ymax (A): -28.30300 17.62300 zmin,zma (A): -43.40700 4.877000 x,y,z range (A): 64.96600 45.92600 48.28400 scale (grids/A): 2.465905 object centre (A): 15.17800 -5.340000 -19.26500 number of atom coordinates read : 3013 total number of charged atoms : 2872 net assigned charge : -1.499979 assigned positive charge : 451.4549 centred at (gu) : 87.24077 90.11623 88.79598 assigned negative charge : -452.9561 centred at (gu) : 86.99426 89.58467 88.30611 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 151394 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27582 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 66778 mr = 106178 m= 18249 mr = 52000 m= 2766 mr = 13262 m= 140 mr = 1630 m= 0 mr = 35 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 2144 time to turn everything in is 0.8000000 number of dielectric boundary points 66222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 22938 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) : 1.643937 object centre at (A) : 15.17800 -5.340000 -19.26500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2657340 0.1003663 midg,1,midg; midg,igrid,midg -4.3074332E-02 5.6635376E-02 1,midg,midg; igrid,midg,midg -0.7236047 0.3454216 gauss-seidel spectral radius is 0.9991528 estimated iterations to convergence 271 setup time was (sec) 1.060000 now iterating at: 14:45:08 rms-change max change #iterations 8.820648 294.2310 at 10iterations 4.953677 141.5496 at 20iterations 2.768221 63.28793 at 30iterations 1.541952 37.58313 at 40iterations 0.8559285 18.15143 at 50iterations 0.4735926 9.755241 at 60iterations 0.2623342 6.072645 at 70iterations 0.1448147 3.232914 at 80iterations 7.9955392E-02 1.900021 at 90iterations 4.4159718E-02 0.9459476 at 100iterations 2.4408065E-02 0.5690384 at 110iterations 1.3462497E-02 0.2981339 at 120iterations 7.4099842E-03 0.1501751 at 130iterations 4.0889801E-03 8.1574440E-02 at 140iterations 2.2599509E-03 4.8426628E-02 at 150iterations 1.2445335E-03 2.5435448E-02 at 160iterations 6.8632246E-04 1.4006615E-02 at 170iterations 3.7882864E-04 8.0757141E-03 at 180iterations finished qdiffx linear iterations at : 14:45:34 total time elapsed so far: 13.57000 # loops : 180 mean,max change (kT/e) : 3.7882864E-04 8.0757141E-03 energy calculations done at 13.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.70000 DelPhi exited at 14:45:35 13.700u 0.248s 0:28.08 49.6% 0+0k 0+0io 0pf+0w