Tue Oct 11 06:00:40 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 Tue Oct 11 2011 at 06:00:41 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7094460 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): 25.87700 72.35300 ymin,ymax (A): -18.67600 31.50400 zmin,zma (A): 4.128000 46.59000 x,y,z range (A): 46.47600 50.18000 42.46200 scale (grids/A): 0.7094460 object centre (A): 49.11500 6.414001 25.35900 number of atom coordinates read : 2327 total number of charged atoms : 1996 net assigned charge : 5.945011 assigned positive charge : 326.1459 centred at (gu) : 89.22639 90.20428 90.27734 assigned negative charge : -320.2010 centred at (gu) : 89.36491 90.14229 90.36076 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7243 nv = 96 ne = 84 npr = 42452 no. pairs analyzed = 42452 no. exposed pairs = 2607 no. arc points = 17829 no. surface atoms = 897 nbur = 1430 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 498 mr = 4178 m= 1 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3469 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1636 ## 140 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8004 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0985672E-08 7.6857685E-09 midg,1,midg; midg,igrid,midg 1.8349393E-08 8.8162153E-08 1,midg,midg; igrid,midg,midg 1.4487047E-07 -1.8832496E-08 gauss-seidel spectral radius is 0.9896468 estimated iterations to convergence 80 setup time was (sec) 0.5400000 now iterating at: 06:00:41 rms-change max change #iterations 0.2041007 38.12477 at 10iterations 2.5992608E-02 3.705715 at 20iterations 3.6203393E-03 0.4615660 at 30iterations 7.0075569E-04 8.3076477E-02 at 40iterations 2.0319359E-04 2.4204254E-02 at 50iterations finished qdiffx linear iterations at : 06:00:44 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 2.0319359E-04 2.4204254E-02 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 06:00:45 3.333u 0.198s 0:04.19 84.0% 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 Tue Oct 11 2011 at 06:00:45 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.128338 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): 25.87700 72.35300 ymin,ymax (A): -18.67600 31.50400 zmin,zma (A): 4.128000 46.59000 x,y,z range (A): 46.47600 50.18000 42.46200 scale (grids/A): 2.128338 object centre (A): 49.11500 6.414001 25.35900 number of atom coordinates read : 2327 total number of charged atoms : 1996 net assigned charge : 5.945011 assigned positive charge : 326.1459 centred at (gu) : 87.67915 90.61290 90.83212 assigned negative charge : -320.2010 centred at (gu) : 88.09473 90.42701 91.08226 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17829 grid for indexing accessible points = 1.400000 m= 31570 mr = 54883 m= 6218 mr = 24134 m= 559 mr = 4102 m= 18 mr = 280 m= 0 mr = 3 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 31940 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 15845 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) : 0.7094460 object centre at (A) : 49.11500 6.414001 25.35900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9929288E-02 2.7093966E-02 midg,1,midg; midg,igrid,midg 4.0072877E-02 2.7860548E-02 1,midg,midg; igrid,midg,midg 4.6461232E-02 -5.2054707E-02 gauss-seidel spectral radius is 0.9988419 estimated iterations to convergence 233 setup time was (sec) 0.8700000 now iterating at: 06:00:46 rms-change max change #iterations 4.677174 209.6102 at 10iterations 2.321485 75.94653 at 20iterations 1.155274 36.34805 at 30iterations 0.5729423 18.42734 at 40iterations 0.2866260 8.619366 at 50iterations 0.1430507 4.396736 at 60iterations 7.1301267E-02 2.128250 at 70iterations 3.5594258E-02 1.191612 at 80iterations 1.7862702E-02 0.5241737 at 90iterations 9.0319859E-03 0.2691088 at 100iterations 4.6058665E-03 0.1335297 at 110iterations 2.4171858E-03 6.8263531E-02 at 120iterations finished qdiffx linear iterations at : 06:00:52 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 2.4171858E-03 6.8263531E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.570000 DelPhi exited at 06:00:53 7.571u 0.200s 0:08.24 94.2% 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 06:00:53 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.192507 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): 25.87700 72.35300 ymin,ymax (A): -18.67600 31.50400 zmin,zma (A): 4.128000 46.59000 x,y,z range (A): 46.47600 50.18000 42.46200 scale (grids/A): 3.192507 object centre (A): 49.11500 6.414001 25.35900 number of atom coordinates read : 2327 total number of charged atoms : 1996 net assigned charge : 5.945011 assigned positive charge : 326.1459 centred at (gu) : 86.51881 90.91936 91.24823 assigned negative charge : -320.2010 centred at (gu) : 87.14204 90.64056 91.62341 start vw surface at 0.1300000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 177509 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17829 grid for indexing accessible points = 1.400000 m= 98037 mr = 132118 m= 40314 mr = 81882 m= 11618 mr = 33211 m= 2405 mr = 9027 m= 317 mr = 1714 m= 23 mr = 203 m= 0 mr = 9 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.820000 number of dielectric boundary points 72059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 15968 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) : 2.128338 object centre at (A) : 49.11500 6.414001 25.35900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1103025 0.2171594 midg,1,midg; midg,igrid,midg 0.3144062 0.1358104 1,midg,midg; igrid,midg,midg 0.4493643 -0.6440817 gauss-seidel spectral radius is 0.9992999 estimated iterations to convergence 298 setup time was (sec) 2.140000 now iterating at: 06:00:55 rms-change max change #iterations 10.42756 354.8632 at 10iterations 6.191084 136.8251 at 20iterations 3.673657 78.06966 at 30iterations 2.169361 42.36118 at 40iterations 1.280374 29.23142 at 50iterations 0.7537012 13.81229 at 60iterations 0.4440758 9.021017 at 70iterations 0.2613801 4.867012 at 80iterations 0.1536062 3.058067 at 90iterations 9.0326883E-02 1.680386 at 100iterations 5.3249862E-02 0.9315300 at 110iterations 3.1608976E-02 0.6030197 at 120iterations 1.8895412E-02 0.3627462 at 130iterations 1.1519063E-02 0.1980553 at 140iterations 7.2570192E-03 0.1464157 at 150iterations 4.7555855E-03 9.2079163E-02 at 160iterations 3.3112690E-03 6.4960480E-02 at 170iterations 2.4404284E-03 4.7004700E-02 at 180iterations finished qdiffx linear iterations at : 06:01:06 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 2.4404284E-03 4.7004700E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 06:01:07 12.897u 0.218s 0:13.54 96.7% 0+0k 0+0io 0pf+0w