Sat Oct 8 17:37:40 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+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 Sat Oct 8 2011 at 17:37:40 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3509 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 0.5244240 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): -0.9420000 44.99000 ymin,ymax (A): -30.33100 26.29000 zmin,zma (A): 1.465000 69.34900 x,y,z range (A): 45.93200 56.62100 67.88400 scale (grids/A): 0.5244240 object centre (A): 22.02400 -2.020501 35.40700 number of atom coordinates read : 3509 total number of charged atoms : 3362 net assigned charge : -5.871980 assigned positive charge : 539.1940 centred at (gu) : 90.41714 91.75917 90.62791 assigned negative charge : -545.0679 centred at (gu) : 90.38154 91.71785 90.61777 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6120 nv = 96 ne = 84 npr = 72047 no. pairs analyzed = 72047 no. exposed pairs = 4232 no. arc points = 29132 no. surface atoms = 1440 nbur = 2069 mkacc time = 0.1600000 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= 204 mr = 3252 m= 0 mr = 10 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3029 ## 462 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8196 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6284922E-10 -1.3962573E-10 midg,1,midg; midg,igrid,midg -1.9279127E-10 -1.2425838E-11 1,midg,midg; igrid,midg,midg -2.5224353E-10 -3.3512727E-11 gauss-seidel spectral radius is 0.9813033 estimated iterations to convergence 60 setup time was (sec) 0.6400000 now iterating at: 17:37:41 rms-change max change #iterations 6.7347698E-02 12.47012 at 10iterations 4.3280451E-03 0.7984648 at 20iterations 4.6169877E-04 7.6693535E-02 at 30iterations 1.1107065E-04 1.9656181E-02 at 40iterations 3.0170495E-05 5.1679611E-03 at 50iterations finished qdiffx linear iterations at : 17:37:45 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 3.0170495E-05 5.1679611E-03 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 17:37:45 4.377u 0.250s 0:04.91 94.0% 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 8 2011 at 17:37:45 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3509 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 1.573272 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): -0.9420000 44.99000 ymin,ymax (A): -30.33100 26.29000 zmin,zma (A): 1.465000 69.34900 x,y,z range (A): 45.93200 56.62100 67.88400 scale (grids/A): 1.573272 object centre (A): 22.02400 -2.020501 35.40700 number of atom coordinates read : 3509 total number of charged atoms : 3362 net assigned charge : -5.871980 assigned positive charge : 539.1940 centred at (gu) : 91.25056 95.27628 91.88271 assigned negative charge : -545.0679 centred at (gu) : 91.14419 95.15334 91.85332 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 68566 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29132 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 20783 mr = 47645 m= 1913 mr = 14229 m= 40 mr = 874 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 28554 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 441 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 25475 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) : 0.5244240 object centre at (A) : 22.02400 -2.020501 35.40700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6819136E-03 1.2686033E-02 midg,1,midg; midg,igrid,midg -7.4439924E-03 -1.0961297E-02 1,midg,midg; igrid,midg,midg -4.6669208E-03 3.1307185E-04 gauss-seidel spectral radius is 0.9980788 estimated iterations to convergence 181 setup time was (sec) 0.8800000 now iterating at: 17:37:47 rms-change max change #iterations 3.396209 149.7747 at 10iterations 1.384948 52.26368 at 20iterations 0.5624822 19.52964 at 30iterations 0.2303485 9.452599 at 40iterations 9.3905859E-02 3.402651 at 50iterations 3.8245603E-02 1.365824 at 60iterations 1.5548987E-02 0.5310364 at 70iterations 6.4010136E-03 0.2219534 at 80iterations 2.6312985E-03 0.1029892 at 90iterations 1.1153637E-03 4.2665303E-02 at 100iterations 4.9304060E-04 1.7942429E-02 at 110iterations 2.3459735E-04 8.1223249E-03 at 120iterations finished qdiffx linear iterations at : 17:37:55 total time elapsed so far: 9.740000 # loops : 120 mean,max change (kT/e) : 2.3459735E-04 8.1223249E-03 energy calculations done at 9.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.920000 DelPhi exited at 17:37:56 9.923u 0.277s 0:10.49 97.1% 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 8 2011 at 17:37:56 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 # of charge parameter records: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3509 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 2.359908 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): -0.9420000 44.99000 ymin,ymax (A): -30.33100 26.29000 zmin,zma (A): 1.465000 69.34900 x,y,z range (A): 45.93200 56.62100 67.88400 scale (grids/A): 2.359908 object centre (A): 22.02400 -2.020501 35.40700 number of atom coordinates read : 3509 total number of charged atoms : 3362 net assigned charge : -5.871980 assigned positive charge : 539.1940 centred at (gu) : 91.87561 97.91428 92.82386 assigned negative charge : -545.0679 centred at (gu) : 91.71641 97.72987 92.77982 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 159952 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29132 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 73465 mr = 117012 m= 19597 mr = 58181 m= 2824 mr = 14598 m= 153 mr = 1775 m= 4 mr = 48 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 64382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 26855 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) : 1.573272 object centre at (A) : 22.02400 -2.020501 35.40700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2046224 9.3377665E-02 midg,1,midg; midg,igrid,midg -0.1008347 -0.1472571 1,midg,midg; igrid,midg,midg -8.1506573E-02 3.2564204E-02 gauss-seidel spectral radius is 0.9991099 estimated iterations to convergence 265 setup time was (sec) 1.710000 now iterating at: 17:37:58 rms-change max change #iterations 9.036189 236.4770 at 10iterations 5.014767 123.2855 at 20iterations 2.767210 74.72167 at 30iterations 1.517359 37.47226 at 40iterations 0.8328955 19.56345 at 50iterations 0.4548637 9.862213 at 60iterations 0.2490137 5.534365 at 70iterations 0.1358045 2.978616 at 80iterations 7.4052088E-02 1.401003 at 90iterations 4.0393218E-02 0.8103647 at 100iterations 2.1974647E-02 0.4239273 at 110iterations 1.2008384E-02 0.2721851 at 120iterations 6.5560578E-03 0.1327147 at 130iterations 3.5883414E-03 8.0533028E-02 at 140iterations 1.9762081E-03 3.7940979E-02 at 150iterations 1.0996149E-03 2.2192955E-02 at 160iterations 6.2319939E-04 1.2486458E-02 at 170iterations 3.6507120E-04 7.4419975E-03 at 180iterations finished qdiffx linear iterations at : 17:38:13 total time elapsed so far: 16.40000 # loops : 180 mean,max change (kT/e) : 3.6507120E-04 7.4419975E-03 energy calculations done at 16.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.58000 DelPhi exited at 17:38:13 16.586u 0.341s 0:17.32 97.6% 0+0k 0+0io 0pf+0w