Tue Oct 11 01:38:07 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 01:38:07 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2610 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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: 0.5954770 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): 18.21400 77.99800 ymin,ymax (A): -10.74900 43.89800 zmin,zma (A): -7.558000 35.11900 x,y,z range (A): 59.78400 54.64700 42.67700 scale (grids/A): 0.5954770 object centre (A): 48.10600 16.57450 13.78050 number of atom coordinates read : 2610 total number of charged atoms : 2461 net assigned charge : 6.812022 assigned positive charge : 391.9908 centred at (gu) : 88.07388 89.65225 89.62058 assigned negative charge : -385.1795 centred at (gu) : 88.32489 89.81466 89.76340 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6162 nv = 96 ne = 84 npr = 52980 no. pairs analyzed = 52980 no. exposed pairs = 3072 no. arc points = 21850 no. surface atoms = 1041 nbur = 1569 mkacc time = 0.1400000 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 = 1.456000 m= 268 mr = 3450 m= 4 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.2900000 number of dielectric boundary points 2954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2156 ## 245 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7606 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3292816E-09 -2.0391246E-09 midg,1,midg; midg,igrid,midg 7.9188789E-09 -2.6419136E-09 1,midg,midg; igrid,midg,midg 1.5584048E-08 -3.6772552E-09 gauss-seidel spectral radius is 0.9854049 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 01:38:08 rms-change max change #iterations 0.1091396 20.29121 at 10iterations 9.9956067E-03 1.875984 at 20iterations 1.4806204E-03 0.3417435 at 30iterations 3.8069402E-04 9.2975616E-02 at 40iterations 1.0436814E-04 2.6203156E-02 at 50iterations finished qdiffx linear iterations at : 01:38:12 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 1.0436814E-04 2.6203156E-02 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 01:38:13 4.464u 0.418s 0:05.55 87.7% 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 01:38:13 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2610 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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: 1.786431 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): 18.21400 77.99800 ymin,ymax (A): -10.74900 43.89800 zmin,zma (A): -7.558000 35.11900 x,y,z range (A): 59.78400 54.64700 42.67700 scale (grids/A): 1.786431 object centre (A): 48.10600 16.57450 13.78050 number of atom coordinates read : 2610 total number of charged atoms : 2461 net assigned charge : 6.812022 assigned positive charge : 391.9908 centred at (gu) : 84.22108 88.95613 88.86105 assigned negative charge : -385.1795 centred at (gu) : 84.97450 89.44382 89.29015 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 67025 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21850 grid for indexing accessible points = 1.400000 m= 22798 mr = 46896 m= 3058 mr = 16924 m= 137 mr = 1831 m= 3 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 2272 time to turn everything in is 0.5300000 number of dielectric boundary points 27320 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 213 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 19173 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) : 0.5954770 object centre at (A) : 48.10600 16.57450 13.78050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0774722E-02 4.3311836E-03 midg,1,midg; midg,igrid,midg 2.2759881E-02 -2.1582114E-02 1,midg,midg; igrid,midg,midg 8.6394129E-03 1.0501617E-03 gauss-seidel spectral radius is 0.9984485 estimated iterations to convergence 201 setup time was (sec) 0.8100000 now iterating at: 01:38:14 rms-change max change #iterations 3.726260 155.3334 at 10iterations 1.659211 70.01218 at 20iterations 0.7373855 25.56647 at 30iterations 0.3285947 11.28260 at 40iterations 0.1464456 5.359425 at 50iterations 6.5483607E-02 2.401796 at 60iterations 2.9453723E-02 1.072145 at 70iterations 1.3348855E-02 0.4464989 at 80iterations 6.1552972E-03 0.2179031 at 90iterations 2.9165244E-03 0.1123810 at 100iterations 1.4886350E-03 6.3812256E-02 at 110iterations 8.1838458E-04 4.0969849E-02 at 120iterations finished qdiffx linear iterations at : 01:38:23 total time elapsed so far: 10.06000 # loops : 120 mean,max change (kT/e) : 8.1838458E-04 4.0969849E-02 energy calculations done at 10.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.24000 DelPhi exited at 01:38:24 10.240u 0.458s 0:11.26 94.9% 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 01:38:24 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: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2610 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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: 2.679647 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): 18.21400 77.99800 ymin,ymax (A): -10.74900 43.89800 zmin,zma (A): -7.558000 35.11900 x,y,z range (A): 59.78400 54.64700 42.67700 scale (grids/A): 2.679647 object centre (A): 48.10600 16.57450 13.78050 number of atom coordinates read : 2610 total number of charged atoms : 2461 net assigned charge : 6.812022 assigned positive charge : 391.9908 centred at (gu) : 81.33163 88.43412 88.29137 assigned negative charge : -385.1795 centred at (gu) : 82.46166 89.16577 88.93506 start vw surface at 0.1200000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 155584 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21850 grid for indexing accessible points = 1.400000 m= 76207 mr = 114036 m= 25120 mr = 62569 m= 5199 mr = 20217 m= 581 mr = 3869 m= 10 mr = 375 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 7449 time to turn everything in is 1.380000 number of dielectric boundary points 61635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 19686 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) : 1.786431 object centre at (A) : 48.10600 16.57450 13.78050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2139998 5.8038302E-02 midg,1,midg; midg,igrid,midg 0.2015306 -0.4143889 1,midg,midg; igrid,midg,midg 4.7958594E-02 0.3841374 gauss-seidel spectral radius is 0.9992021 estimated iterations to convergence 280 setup time was (sec) 1.710000 now iterating at: 01:38:26 rms-change max change #iterations 8.982713 292.0912 at 10iterations 5.128520 125.7327 at 20iterations 2.893435 65.14240 at 30iterations 1.637270 39.32948 at 40iterations 0.9232188 18.83205 at 50iterations 0.5206901 10.40866 at 60iterations 0.2933341 5.859788 at 70iterations 0.1649137 3.397660 at 80iterations 9.2880204E-02 1.988474 at 90iterations 5.2378345E-02 1.077162 at 100iterations 2.9578008E-02 0.6153908 at 110iterations 1.6736152E-02 0.3329697 at 120iterations 9.5512336E-03 0.2006912 at 130iterations 5.5127959E-03 0.1327934 at 140iterations 3.2520748E-03 7.4962616E-02 at 150iterations 1.9922829E-03 5.0800323E-02 at 160iterations 1.2896686E-03 3.4912109E-02 at 170iterations 8.8123250E-04 2.3933411E-02 at 180iterations finished qdiffx linear iterations at : 01:38:42 total time elapsed so far: 17.21000 # loops : 180 mean,max change (kT/e) : 8.8123250E-04 2.3933411E-02 energy calculations done at 17.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.37000 DelPhi exited at 01:38:43 17.371u 0.485s 0:18.43 96.8% 0+0k 0+0io 0pf+0w