Mon Oct 10 17:06:09 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 17:06:10 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 !!! WARNING: ASL 152 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5464816 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): -2.588000 39.53800 ymin,ymax (A): -9.268001 41.68900 zmin,zma (A): -2.580000 62.56400 x,y,z range (A): 42.12600 50.95700 65.14400 scale (grids/A): 0.5464816 object centre (A): 18.47500 16.21050 29.99200 number of atom coordinates read : 2637 total number of charged atoms : 2500 net assigned charge : 6.900024 assigned positive charge : 393.0686 centred at (gu) : 89.68012 89.42735 89.59219 assigned negative charge : -386.1697 centred at (gu) : 89.77003 89.35564 89.62402 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5129 nv = 96 ne = 84 npr = 52758 no. pairs analyzed = 52758 no. exposed pairs = 3529 no. arc points = 25041 no. surface atoms = 1188 nbur = 1449 mkacc time = 0.1700000 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= 223 mr = 2480 m= 0 mr = 10 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 2862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2561 ## 338 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 6693 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9043360E-10 2.2803233E-10 midg,1,midg; midg,igrid,midg 1.1308210E-11 7.4460532E-10 1,midg,midg; igrid,midg,midg 1.0405009E-09 -8.7488135E-11 gauss-seidel spectral radius is 0.9827128 estimated iterations to convergence 63 setup time was (sec) 0.6800000 now iterating at: 17:06:11 rms-change max change #iterations 7.0504323E-02 15.40217 at 10iterations 4.7599045E-03 0.7973690 at 20iterations 3.5664570E-04 5.3901672E-02 at 30iterations 3.5636785E-05 5.6457520E-03 at 40iterations 5.1730499E-06 7.9917908E-04 at 50iterations finished qdiffx linear iterations at : 17:06:14 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 5.1730499E-06 7.9917908E-04 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 17:06:15 4.546u 0.425s 0:05.59 88.7% 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 17:06:15 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 !!! WARNING: ASL 152 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.639445 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): -2.588000 39.53800 ymin,ymax (A): -9.268001 41.68900 zmin,zma (A): -2.580000 62.56400 x,y,z range (A): 42.12600 50.95700 65.14400 scale (grids/A): 1.639445 object centre (A): 18.47500 16.21050 29.99200 number of atom coordinates read : 2637 total number of charged atoms : 2500 net assigned charge : 6.900024 assigned positive charge : 393.0686 centred at (gu) : 89.03966 88.28169 88.77603 assigned negative charge : -386.1697 centred at (gu) : 89.31002 88.06677 88.87196 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 56417 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25041 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 16911 mr = 36722 m= 1817 mr = 11227 m= 52 mr = 826 m= 0 mr = 10 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 178 time to turn everything in is 0.6000000 number of dielectric boundary points 26412 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 262 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 19147 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) : 0.5464816 object centre at (A) : 18.47500 16.21050 29.99200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8206080E-02 1.8925687E-02 midg,1,midg; midg,igrid,midg -5.6389272E-03 7.5482036E-04 1,midg,midg; igrid,midg,midg 8.7988377E-03 -1.8400958E-04 gauss-seidel spectral radius is 0.9981678 estimated iterations to convergence 186 setup time was (sec) 0.9400000 now iterating at: 17:06:17 rms-change max change #iterations 3.097934 133.0316 at 10iterations 1.284372 51.05505 at 20iterations 0.5307204 21.38955 at 30iterations 0.2204867 8.143700 at 40iterations 9.1353148E-02 3.386468 at 50iterations 3.7873361E-02 1.477944 at 60iterations 1.5799766E-02 0.5834856 at 70iterations 6.5551926E-03 0.2615623 at 80iterations 2.7292219E-03 0.1046867 at 90iterations 1.1342287E-03 4.4239998E-02 at 100iterations 4.7314368E-04 1.7665863E-02 at 110iterations 1.9861689E-04 7.1582794E-03 at 120iterations finished qdiffx linear iterations at : 17:06:26 total time elapsed so far: 10.08000 # loops : 120 mean,max change (kT/e) : 1.9861689E-04 7.1582794E-03 energy calculations done at 10.08000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.31000 DelPhi exited at 17:06:26 10.317u 0.456s 0:11.21 95.9% 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 17:06:26 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2637 !!! WARNING: ASL 152 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.459167 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): -2.588000 39.53800 ymin,ymax (A): -9.268001 41.68900 zmin,zma (A): -2.580000 62.56400 x,y,z range (A): 42.12600 50.95700 65.14400 scale (grids/A): 2.459167 object centre (A): 18.47500 16.21050 29.99200 number of atom coordinates read : 2637 total number of charged atoms : 2500 net assigned charge : 6.900024 assigned positive charge : 393.0686 centred at (gu) : 88.55936 87.42232 88.16392 assigned negative charge : -386.1697 centred at (gu) : 88.96498 87.10005 88.30803 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 130716 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25041 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 58728 mr = 90254 m= 16729 mr = 45284 m= 2778 mr = 12253 m= 170 mr = 1706 m= 5 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 606 time to turn everything in is 1.450000 number of dielectric boundary points 59569 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.600000 number of grid points assigned charge 19964 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) : 1.639445 object centre at (A) : 18.47500 16.21050 29.99200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2231251 0.4946833 midg,1,midg; midg,igrid,midg -5.0537124E-02 -8.4265526E-03 1,midg,midg; igrid,midg,midg 0.1150652 -9.5236389E-04 gauss-seidel spectral radius is 0.9991314 estimated iterations to convergence 268 setup time was (sec) 1.800000 now iterating at: 17:06:29 rms-change max change #iterations 8.235320 333.8293 at 10iterations 4.649307 157.1040 at 20iterations 2.603158 67.18875 at 30iterations 1.450392 37.29881 at 40iterations 0.8050669 19.13380 at 50iterations 0.4456879 10.86381 at 60iterations 0.2458990 6.028299 at 70iterations 0.1355846 3.223185 at 80iterations 7.4576914E-02 1.569259 at 90iterations 4.0865030E-02 0.9412785 at 100iterations 2.2474073E-02 0.5171871 at 110iterations 1.2353312E-02 0.2872772 at 120iterations 6.7757382E-03 0.1537056 at 130iterations 3.7145561E-03 8.7815166E-02 at 140iterations 2.0405264E-03 4.9964905E-02 at 150iterations 1.1158698E-03 2.4111748E-02 at 160iterations 6.1330234E-04 1.3458252E-02 at 170iterations 3.3713074E-04 7.4005127E-03 at 180iterations finished qdiffx linear iterations at : 17:06:44 total time elapsed so far: 17.12000 # loops : 180 mean,max change (kT/e) : 3.3713074E-04 7.4005127E-03 energy calculations done at 17.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.33000 DelPhi exited at 17:06:45 17.334u 0.500s 0:18.32 97.3% 0+0k 0+0io 0pf+0w