Tue Oct 11 08:06:53 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 Tue Oct 11 2011 at 08:06:53 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2333 !!! WARNING: MG9 902 has a net charge of 1.4000 !!! WARNING: MG9 903 has a net charge of 1.4000 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: 0.6049483 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): -22.81500 25.50200 ymin,ymax (A): 22.21000 81.05800 zmin,zma (A): 2.162000 51.56200 x,y,z range (A): 48.31700 58.84800 49.40000 scale (grids/A): 0.6049483 object centre (A): 1.343499 51.63400 26.86200 number of atom coordinates read : 2333 total number of charged atoms : 2195 net assigned charge : 7.300011 assigned positive charge : 352.9723 centred at (gu) : 91.02621 87.40422 92.08674 assigned negative charge : -345.6729 centred at (gu) : 90.91954 87.37593 91.98077 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5640 nv = 96 ne = 84 npr = 47318 no. pairs analyzed = 47318 no. exposed pairs = 3123 no. arc points = 21740 no. surface atoms = 1044 nbur = 1289 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 261 mr = 2817 m= 4 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3056 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2209 ## 234 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6973 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4813399E-10 1.1905104E-08 midg,1,midg; midg,igrid,midg 4.2926378E-09 2.6014610E-09 1,midg,midg; igrid,midg,midg -3.7198175E-10 9.3803774E-09 gauss-seidel spectral radius is 0.9858353 estimated iterations to convergence 69 setup time was (sec) 0.6000000 now iterating at: 08:06:54 rms-change max change #iterations 0.1097930 16.41059 at 10iterations 9.4591053E-03 1.780472 at 20iterations 9.0741855E-04 0.1442108 at 30iterations 1.4355253E-04 3.5398483E-02 at 40iterations 3.9898750E-05 1.0509491E-02 at 50iterations finished qdiffx linear iterations at : 08:06:57 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 3.9898750E-05 1.0509491E-02 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 08:06:58 4.151u 0.259s 0:04.77 92.2% 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 Oct 11 2011 at 08:06:58 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2333 !!! WARNING: MG9 902 has a net charge of 1.4000 !!! WARNING: MG9 903 has a net charge of 1.4000 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: 1.814845 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): -22.81500 25.50200 ymin,ymax (A): 22.21000 81.05800 zmin,zma (A): 2.162000 51.56200 x,y,z range (A): 48.31700 58.84800 49.40000 scale (grids/A): 1.814845 object centre (A): 1.343499 51.63400 26.86200 number of atom coordinates read : 2333 total number of charged atoms : 2195 net assigned charge : 7.300011 assigned positive charge : 352.9723 centred at (gu) : 93.07829 82.21248 96.26003 assigned negative charge : -345.6729 centred at (gu) : 92.75848 82.12784 95.94236 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 61141 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21740 grid for indexing accessible points = 1.400000 m= 19936 mr = 40519 m= 2726 mr = 13739 m= 142 mr = 1549 m= 3 mr = 43 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 0.5700000 number of dielectric boundary points 28098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 17127 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) : 0.6049483 object centre at (A) : 1.343499 51.63400 26.86200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.7143747E-04 2.5165506E-02 midg,1,midg; midg,igrid,midg 3.4428388E-02 2.9684355E-02 1,midg,midg; igrid,midg,midg -1.8708791E-03 2.2218540E-02 gauss-seidel spectral radius is 0.9984661 estimated iterations to convergence 203 setup time was (sec) 0.8700000 now iterating at: 08:06:59 rms-change max change #iterations 3.646052 153.6159 at 10iterations 1.624903 61.84203 at 20iterations 0.7236218 25.94844 at 30iterations 0.3224507 12.18442 at 40iterations 0.1437984 5.211029 at 50iterations 6.4649485E-02 2.199863 at 60iterations 2.8997624E-02 1.042938 at 70iterations 1.2951221E-02 0.4600677 at 80iterations 5.8195670E-03 0.2244473 at 90iterations 2.6427577E-03 0.1011772 at 100iterations 1.2365715E-03 4.7397614E-02 at 110iterations 6.0171430E-04 2.5825500E-02 at 120iterations finished qdiffx linear iterations at : 08:07:08 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 6.0171430E-04 2.5825500E-02 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 08:07:08 9.536u 0.298s 0:10.36 94.7% 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 Tue Oct 11 2011 at 08:07:09 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 # of charge parameter records: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2333 !!! WARNING: MG9 902 has a net charge of 1.4000 !!! WARNING: MG9 903 has a net charge of 1.4000 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: 2.722268 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): -22.81500 25.50200 ymin,ymax (A): 22.21000 81.05800 zmin,zma (A): 2.162000 51.56200 x,y,z range (A): 48.31700 58.84800 49.40000 scale (grids/A): 2.722268 object centre (A): 1.343499 51.63400 26.86200 number of atom coordinates read : 2333 total number of charged atoms : 2195 net assigned charge : 7.300011 assigned positive charge : 352.9723 centred at (gu) : 94.61725 78.31846 99.38981 assigned negative charge : -345.6729 centred at (gu) : 94.13771 78.19173 98.91354 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 141769 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21740 grid for indexing accessible points = 1.400000 m= 66275 mr = 99154 m= 21663 mr = 52315 m= 4652 mr = 16329 m= 595 mr = 3408 m= 24 mr = 383 m= 0 mr = 4 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.400000 number of dielectric boundary points 63385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 17553 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) : 1.814845 object centre at (A) : 1.343499 51.63400 26.86200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.8251002E-02 0.2677820 midg,1,midg; midg,igrid,midg 0.4670809 0.3955071 1,midg,midg; igrid,midg,midg -1.3452021E-02 0.2296208 gauss-seidel spectral radius is 0.9992136 estimated iterations to convergence 282 setup time was (sec) 1.740000 now iterating at: 08:07:11 rms-change max change #iterations 8.982224 283.9691 at 10iterations 5.233299 155.1051 at 20iterations 2.999459 66.45830 at 30iterations 1.716421 41.10148 at 40iterations 0.9777626 21.81659 at 50iterations 0.5558417 12.66877 at 60iterations 0.3153885 6.367708 at 70iterations 0.1788063 3.765299 at 80iterations 0.1014202 2.243952 at 90iterations 5.7362124E-02 1.273578 at 100iterations 3.2432605E-02 0.6476240 at 110iterations 1.8391682E-02 0.3785588 at 120iterations 1.0437133E-02 0.2130928 at 130iterations 5.9389342E-03 0.1242743 at 140iterations 3.4167797E-03 7.6410294E-02 at 150iterations 1.9947938E-03 4.8807144E-02 at 160iterations 1.1974667E-03 3.1436920E-02 at 170iterations 7.4815308E-04 2.0504951E-02 at 180iterations finished qdiffx linear iterations at : 08:07:24 total time elapsed so far: 15.49000 # loops : 180 mean,max change (kT/e) : 7.4815308E-04 2.0504951E-02 energy calculations done at 15.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.67000 DelPhi exited at 08:07:25 15.669u 0.303s 0:16.38 97.4% 0+0k 0+0io 0pf+0w