Tue Nov 1 10:40:55 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 Tue Nov 1 2011 at 10:40:56 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 ! Automatically converted by prot2crg.py # of charge parameter records: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3229 !!! WARNING: NAP 528 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: 0.5227300 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): 20.49900 88.60300 ymin,ymax (A): -7.472000 48.14600 zmin,zma (A): 23.49000 74.36800 x,y,z range (A): 68.10400 55.61800 50.87801 scale (grids/A): 0.5227300 object centre (A): 54.55100 20.33700 48.92900 number of atom coordinates read : 3229 total number of charged atoms : 3091 net assigned charge : 5.000031 assigned positive charge : 482.4337 centred at (gu) : 88.72520 90.59366 90.22685 assigned negative charge : -477.4351 centred at (gu) : 88.62843 90.63747 90.18795 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5697 nv = 96 ne = 84 npr = 65677 no. pairs analyzed = 65677 no. exposed pairs = 3996 no. arc points = 27986 no. surface atoms = 1337 nbur = 1892 mkacc time = 0.1100000 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 = 1.624000 m= 207 mr = 2972 m= 0 mr = 9 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 2923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2778 ## 373 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7550 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2208222E-11 2.5018959E-10 midg,1,midg; midg,igrid,midg 2.1484511E-10 -2.8862845E-12 1,midg,midg; igrid,midg,midg -2.2177156E-10 2.8797609E-10 gauss-seidel spectral radius is 0.9811690 estimated iterations to convergence 60 setup time was (sec) 0.4200000 now iterating at: 10:40:56 rms-change max change #iterations 5.9302192E-02 12.91136 at 10iterations 3.6369939E-03 0.6756229 at 20iterations 2.7202058E-04 4.7557831E-02 at 30iterations 3.6045727E-05 4.9629211E-03 at 40iterations 6.8371023E-06 9.6130371E-04 at 50iterations finished qdiffx linear iterations at : 10:41:00 total time elapsed so far: 3.680000 # loops : 50 mean,max change (kT/e) : 6.8371023E-06 9.6130371E-04 energy calculations done at 3.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.820000 DelPhi exited at 10:41:00 3.826u 0.192s 0:04.47 89.7% 0+0k 0+0io 6pf+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 Tue Nov 1 2011 at 10:41:00 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 ! Automatically converted by prot2crg.py # of charge parameter records: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3229 !!! WARNING: NAP 528 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.568190 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): 20.49900 88.60300 ymin,ymax (A): -7.472000 48.14600 zmin,zma (A): 23.49000 74.36800 x,y,z range (A): 68.10400 55.61800 50.87801 scale (grids/A): 1.568190 object centre (A): 54.55100 20.33700 48.92900 number of atom coordinates read : 3229 total number of charged atoms : 3091 net assigned charge : 5.000031 assigned positive charge : 482.4337 centred at (gu) : 86.17487 91.78003 90.67969 assigned negative charge : -477.4351 centred at (gu) : 85.88507 91.91201 90.56349 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 64440 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27986 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18500 mr = 44387 m= 1583 mr = 12323 m= 39 mr = 668 m= 0 mr = 4 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 989 time to turn everything in is 0.3400000 number of dielectric boundary points 27180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 324 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 23424 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) : 0.5227300 object centre at (A) : 54.55100 20.33700 48.92900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8115148E-03 7.8575555E-03 midg,1,midg; midg,igrid,midg 5.2612131E-03 2.3408236E-03 1,midg,midg; igrid,midg,midg -1.1721001E-02 6.2281578E-03 gauss-seidel spectral radius is 0.9980530 estimated iterations to convergence 180 setup time was (sec) 0.5600000 now iterating at: 10:41:01 rms-change max change #iterations 3.174529 142.3590 at 10iterations 1.288272 48.85819 at 20iterations 0.5203639 19.44070 at 30iterations 0.2107277 7.592437 at 40iterations 8.4994823E-02 3.263250 at 50iterations 3.4340099E-02 1.270971 at 60iterations 1.3954169E-02 0.4888783 at 70iterations 5.6499187E-03 0.2019587 at 80iterations 2.2923122E-03 8.7762833E-02 at 90iterations 9.3117531E-04 3.4257889E-02 at 100iterations 3.7960309E-04 1.4599800E-02 at 110iterations 1.5600777E-04 6.4926147E-03 at 120iterations finished qdiffx linear iterations at : 10:41:08 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 1.5600777E-04 6.4926147E-03 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 10:41:09 7.826u 0.250s 0:08.46 95.3% 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 Tue Nov 1 2011 at 10:41:09 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 ! Automatically converted by prot2crg.py # of charge parameter records: 339 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3229 !!! WARNING: NAP 528 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.352285 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): 20.49900 88.60300 ymin,ymax (A): -7.472000 48.14600 zmin,zma (A): 23.49000 74.36800 x,y,z range (A): 68.10400 55.61800 50.87801 scale (grids/A): 2.352285 object centre (A): 54.55100 20.33700 48.92900 number of atom coordinates read : 3229 total number of charged atoms : 3091 net assigned charge : 5.000031 assigned positive charge : 482.4337 centred at (gu) : 84.26215 92.66978 91.01948 assigned negative charge : -477.4351 centred at (gu) : 83.82745 92.86794 90.84514 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 150208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27986 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 66579 mr = 109099 m= 16736 mr = 52126 m= 2310 mr = 11973 m= 160 mr = 1397 m= 3 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 3572 time to turn everything in is 0.7700000 number of dielectric boundary points 61338 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 24680 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) : 1.568190 object centre at (A) : 54.55100 20.33700 48.92900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7356261E-02 0.1421329 midg,1,midg; midg,igrid,midg 7.4783795E-02 2.1592533E-02 1,midg,midg; igrid,midg,midg -0.3130356 5.3308450E-02 gauss-seidel spectral radius is 0.9991025 estimated iterations to convergence 264 setup time was (sec) 1.020000 now iterating at: 10:41:10 rms-change max change #iterations 8.371632 263.6121 at 10iterations 4.673254 136.5646 at 20iterations 2.585387 61.09709 at 30iterations 1.424993 32.29873 at 40iterations 0.7810712 17.85718 at 50iterations 0.4286193 9.676440 at 60iterations 0.2342345 5.662205 at 70iterations 0.1280003 2.870619 at 80iterations 6.9884941E-02 1.510965 at 90iterations 3.8033906E-02 0.8661366 at 100iterations 2.0729005E-02 0.4711175 at 110iterations 1.1262147E-02 0.2608528 at 120iterations 6.1285445E-03 0.1359661 at 130iterations 3.3320384E-03 7.1113110E-02 at 140iterations 1.8113804E-03 3.9102554E-02 at 150iterations 9.8379992E-04 2.0616531E-02 at 160iterations 5.3633039E-04 1.1169434E-02 at 170iterations 2.9126299E-04 6.2201023E-03 at 180iterations finished qdiffx linear iterations at : 10:41:22 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 2.9126299E-04 6.2201023E-03 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 10:41:22 12.361u 0.478s 0:13.72 93.5% 0+0k 0+0io 0pf+0w