Sun Oct 9 19:53:44 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 19:53:44 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3514 !!! WARNING: HIT 614 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5693085 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): 6.472000 66.52400 ymin,ymax (A): 1.702000 61.88100 zmin,zma (A): -0.6970000 61.83500 x,y,z range (A): 60.05200 60.17900 62.53200 scale (grids/A): 0.5693085 object centre (A): 36.49800 31.79150 30.56900 number of atom coordinates read : 3514 total number of charged atoms : 3365 net assigned charge : -0.3649753 assigned positive charge : 533.1187 centred at (gu) : 88.65983 88.39362 88.80827 assigned negative charge : -533.4855 centred at (gu) : 88.61382 88.46349 88.76701 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7776 nv = 96 ne = 84 npr = 66762 no. pairs analyzed = 66762 no. exposed pairs = 4771 no. arc points = 33407 no. surface atoms = 1604 nbur = 1910 mkacc time = 0.1500000 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 = 1.512000 m= 389 mr = 3989 m= 0 mr = 22 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 4154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3290 ## 361 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9811 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0856996E-09 5.2255789E-10 midg,1,midg; midg,igrid,midg 1.7991624E-09 -9.1353325E-10 1,midg,midg; igrid,midg,midg -1.2477382E-09 5.6651878E-10 gauss-seidel spectral radius is 0.9841334 estimated iterations to convergence 65 setup time was (sec) 0.5500000 now iterating at: 19:53:45 rms-change max change #iterations 9.9722639E-02 16.98018 at 10iterations 7.7732378E-03 1.127635 at 20iterations 1.1907865E-03 0.1576920 at 30iterations 6.4182660E-04 7.0497990E-02 at 40iterations 4.1018822E-04 4.6656847E-02 at 50iterations finished qdiffx linear iterations at : 19:53:47 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 4.1018822E-04 4.6656847E-02 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 19:53:48 3.121u 0.145s 0:03.58 91.0% 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 Sun Oct 9 2011 at 19:53:48 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3514 !!! WARNING: HIT 614 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.707926 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): 6.472000 66.52400 ymin,ymax (A): 1.702000 61.88100 zmin,zma (A): -0.6970000 61.83500 x,y,z range (A): 60.05200 60.17900 62.53200 scale (grids/A): 1.707926 object centre (A): 36.49800 31.79150 30.56900 number of atom coordinates read : 3514 total number of charged atoms : 3365 net assigned charge : -0.3649753 assigned positive charge : 533.1187 centred at (gu) : 85.97820 85.17953 86.42387 assigned negative charge : -533.4855 centred at (gu) : 85.84098 85.39007 86.30051 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 85200 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33407 grid for indexing accessible points = 1.400000 m= 29631 mr = 57825 m= 4011 mr = 20507 m= 158 mr = 2166 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 38482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 275 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 26075 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) : 0.5693085 object centre at (A) : 36.49800 31.79150 30.56900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1753702E-02 -9.9918833E-03 midg,1,midg; midg,igrid,midg 1.7877158E-02 -5.7927421E-03 1,midg,midg; igrid,midg,midg -4.3668905E-03 3.5174901E-04 gauss-seidel spectral radius is 0.9984130 estimated iterations to convergence 199 setup time was (sec) 0.8600000 now iterating at: 19:53:49 rms-change max change #iterations 4.150511 168.2222 at 10iterations 1.839469 63.72700 at 20iterations 0.8163955 31.19417 at 30iterations 0.3611580 11.41648 at 40iterations 0.1598177 4.896370 at 50iterations 7.1088240E-02 2.268550 at 60iterations 3.1567622E-02 1.257447 at 70iterations 1.4035041E-02 0.5035477 at 80iterations 6.3575003E-03 0.1936507 at 90iterations 3.0063612E-03 9.7095490E-02 at 100iterations 1.6018432E-03 5.0140381E-02 at 110iterations 1.0382854E-03 2.9651642E-02 at 120iterations finished qdiffx linear iterations at : 19:53:55 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 1.0382854E-03 2.9651642E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.960000 DelPhi exited at 19:53:55 6.959u 0.152s 0:07.45 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 Sun Oct 9 2011 at 19:53:55 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3514 !!! WARNING: HIT 614 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.561888 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): 6.472000 66.52400 ymin,ymax (A): 1.702000 61.88100 zmin,zma (A): -0.6970000 61.83500 x,y,z range (A): 60.05200 60.17900 62.53200 scale (grids/A): 2.561888 object centre (A): 36.49800 31.79150 30.56900 number of atom coordinates read : 3514 total number of charged atoms : 3365 net assigned charge : -0.3649753 assigned positive charge : 533.1187 centred at (gu) : 83.96694 82.76896 84.63537 assigned negative charge : -533.4855 centred at (gu) : 83.76144 83.08495 84.45083 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 197345 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33407 grid for indexing accessible points = 1.400000 m= 97910 mr = 141290 m= 32675 mr = 77406 m= 6863 mr = 24800 m= 596 mr = 4628 m= 17 mr = 288 m= 0 mr = 0 time to grow re-entrant surface = 0.8699999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.430000 number of dielectric boundary points 86994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 26903 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) : 1.707926 object centre at (A) : 36.49800 31.79150 30.56900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2081510 -4.9870145E-02 midg,1,midg; midg,igrid,midg 0.2028283 -8.6752355E-02 1,midg,midg; igrid,midg,midg 1.2334576E-02 -1.3745577E-02 gauss-seidel spectral radius is 0.9992297 estimated iterations to convergence 284 setup time was (sec) 1.710000 now iterating at: 19:53:57 rms-change max change #iterations 10.70085 342.0513 at 10iterations 6.393259 158.0888 at 20iterations 3.760058 97.13824 at 30iterations 2.194299 45.85613 at 40iterations 1.276176 28.06855 at 50iterations 0.7386484 17.30980 at 60iterations 0.4267947 8.181434 at 70iterations 0.2451046 4.887460 at 80iterations 0.1407782 2.890421 at 90iterations 8.0994114E-02 1.691994 at 100iterations 4.6351846E-02 0.8645059 at 110iterations 2.6596019E-02 0.5127010 at 120iterations 1.5181812E-02 0.2911072 at 130iterations 8.6886827E-03 0.1753426 at 140iterations 4.9665770E-03 9.5272064E-02 at 150iterations 2.8378943E-03 5.5244446E-02 at 160iterations 1.6290236E-03 2.9548645E-02 at 170iterations 9.3683036E-04 2.0042419E-02 at 180iterations finished qdiffx linear iterations at : 19:54:07 total time elapsed so far: 11.48000 # loops : 180 mean,max change (kT/e) : 9.3683036E-04 2.0042419E-02 energy calculations done at 11.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.65000 DelPhi exited at 19:54:07 11.655u 0.186s 0:12.11 97.6% 0+0k 0+0io 0pf+0w