Sun Oct 9 07:18:22 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 Sun Oct 9 2011 at 07:18:22 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2512 !!! WARNING: PRO 130 has a net charge of 0.5000 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: 0.5459872 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): -4.495000 42.18900 ymin,ymax (A): 36.86000 87.36600 zmin,zma (A): -3.179000 62.02400 x,y,z range (A): 46.68400 50.50600 65.20300 scale (grids/A): 0.5459872 object centre (A): 18.84700 62.11300 29.42250 number of atom coordinates read : 2512 total number of charged atoms : 2367 net assigned charge : -7.999978 assigned positive charge : 376.0409 centred at (gu) : 90.56450 88.92813 89.51011 assigned negative charge : -384.0414 centred at (gu) : 90.71204 88.56938 89.41637 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4972 nv = 96 ne = 84 npr = 49972 no. pairs analyzed = 49972 no. exposed pairs = 3550 no. arc points = 25281 no. surface atoms = 1190 nbur = 1322 mkacc time = 0.1300000 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= 206 mr = 2346 m= 2 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2830 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2470 ## 315 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6388 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1312674E-09 6.0328596E-11 midg,1,midg; midg,igrid,midg -3.4171157E-09 1.1467435E-09 1,midg,midg; igrid,midg,midg 3.1823474E-10 -1.5186675E-09 gauss-seidel spectral radius is 0.9826764 estimated iterations to convergence 63 setup time was (sec) 0.5900000 now iterating at: 07:18:23 rms-change max change #iterations 6.6807240E-02 12.31095 at 10iterations 4.3442762E-03 0.7277718 at 20iterations 2.8563946E-04 4.7779083E-02 at 30iterations 2.0374524E-05 3.8833618E-03 at 40iterations 2.0045536E-06 3.5262108E-04 at 50iterations finished qdiffx linear iterations at : 07:18:26 total time elapsed so far: 4.390000 # loops : 50 mean,max change (kT/e) : 2.0045536E-06 3.5262108E-04 energy calculations done at 4.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.550000 DelPhi exited at 07:18:27 4.559u 0.394s 0:05.21 94.8% 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 Sun Oct 9 2011 at 07:18:27 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2512 !!! WARNING: PRO 130 has a net charge of 0.5000 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: 1.637962 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): -4.495000 42.18900 ymin,ymax (A): 36.86000 87.36600 zmin,zma (A): -3.179000 62.02400 x,y,z range (A): 46.68400 50.50600 65.20300 scale (grids/A): 1.637962 object centre (A): 18.84700 62.11300 29.42250 number of atom coordinates read : 2512 total number of charged atoms : 2367 net assigned charge : -7.999978 assigned positive charge : 376.0409 centred at (gu) : 91.69309 86.78384 88.53030 assigned negative charge : -384.0414 centred at (gu) : 92.13581 85.70771 88.24892 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 54677 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25281 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 16134 mr = 34731 m= 1398 mr = 10573 m= 35 mr = 593 m= 0 mr = 2 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 298 time to turn everything in is 0.4600000 number of dielectric boundary points 26345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 267 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 18176 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) : 0.5459872 object centre at (A) : 18.84700 62.11300 29.42250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3590414E-02 3.4850955E-03 midg,1,midg; midg,igrid,midg -2.2885062E-02 7.8655202E-03 1,midg,midg; igrid,midg,midg -2.1738720E-03 -1.3016348E-02 gauss-seidel spectral radius is 0.9981496 estimated iterations to convergence 185 setup time was (sec) 0.7400000 now iterating at: 07:18:28 rms-change max change #iterations 3.055203 162.3799 at 10iterations 1.260199 56.02097 at 20iterations 0.5169997 20.62275 at 30iterations 0.2141650 9.268247 at 40iterations 8.8499770E-02 3.554749 at 50iterations 3.6452759E-02 1.510344 at 60iterations 1.5010478E-02 0.6438160 at 70iterations 6.1966889E-03 0.2377272 at 80iterations 2.5596581E-03 0.1113787 at 90iterations 1.0606061E-03 4.5811892E-02 at 100iterations 4.3661523E-04 1.5755653E-02 at 110iterations 1.8075141E-04 6.8035126E-03 at 120iterations finished qdiffx linear iterations at : 07:18:38 total time elapsed so far: 10.51000 # loops : 120 mean,max change (kT/e) : 1.8075141E-04 6.8035126E-03 energy calculations done at 10.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.00000 DelPhi exited at 07:18:39 11.000u 0.454s 0:11.73 97.6% 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 Sun Oct 9 2011 at 07:18:39 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2512 !!! WARNING: PRO 130 has a net charge of 0.5000 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: 2.456942 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): -4.495000 42.18900 ymin,ymax (A): 36.86000 87.36600 zmin,zma (A): -3.179000 62.02400 x,y,z range (A): 46.68400 50.50600 65.20300 scale (grids/A): 2.456942 object centre (A): 18.84700 62.11300 29.42250 number of atom coordinates read : 2512 total number of charged atoms : 2367 net assigned charge : -7.999978 assigned positive charge : 376.0409 centred at (gu) : 92.53956 85.17551 87.79524 assigned negative charge : -384.0414 centred at (gu) : 93.20370 83.56145 87.37329 start vw surface at 0.1300000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 126548 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25281 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 56416 mr = 85212 m= 14828 mr = 43469 m= 2021 mr = 10558 m= 113 mr = 1187 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 1064 time to turn everything in is 1.110000 number of dielectric boundary points 59466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 18911 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) : 1.637962 object centre at (A) : 18.84700 62.11300 29.42250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9316352 2.7314853E-02 midg,1,midg; midg,igrid,midg -0.3067828 0.1087327 1,midg,midg; igrid,midg,midg -3.5661310E-02 -0.1746531 gauss-seidel spectral radius is 0.9991206 estimated iterations to convergence 266 setup time was (sec) 1.420000 now iterating at: 07:18:41 rms-change max change #iterations 8.032778 338.6702 at 10iterations 4.480857 140.1592 at 20iterations 2.504769 64.77296 at 30iterations 1.383053 36.38058 at 40iterations 0.7661554 20.89935 at 50iterations 0.4221832 11.35144 at 60iterations 0.2324794 5.561410 at 70iterations 0.1273533 3.120060 at 80iterations 7.0004120E-02 1.883431 at 90iterations 3.8372945E-02 0.8643171 at 100iterations 2.0988712E-02 0.5224447 at 110iterations 1.1503499E-02 0.2500935 at 120iterations 6.2833405E-03 0.1529083 at 130iterations 3.4357728E-03 8.8737488E-02 at 140iterations 1.8760244E-03 4.1194916E-02 at 150iterations 1.0243136E-03 2.2274017E-02 at 160iterations 5.5943354E-04 1.2668610E-02 at 170iterations 3.0563812E-04 6.8702698E-03 at 180iterations finished qdiffx linear iterations at : 07:18:57 total time elapsed so far: 17.69000 # loops : 180 mean,max change (kT/e) : 3.0563812E-04 6.8702698E-03 energy calculations done at 17.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.85000 DelPhi exited at 07:18:57 17.859u 0.475s 0:18.62 98.3% 0+0k 0+0io 0pf+0w