Sat Oct 8 17:49:36 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 17:49:37 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5222468 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): 41.21800 109.3850 ymin,ymax (A): 10.32300 56.99900 zmin,zma (A): 2.670000 51.21100 x,y,z range (A): 68.16701 46.67599 48.54100 scale (grids/A): 0.5222468 object centre (A): 75.30150 33.66100 26.94050 number of atom coordinates read : 3305 total number of charged atoms : 3162 net assigned charge : -0.9999930 assigned positive charge : 499.5877 centred at (gu) : 90.26537 88.87607 90.23458 assigned negative charge : -500.5891 centred at (gu) : 90.28066 88.75504 90.22353 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5828 nv = 96 ne = 84 npr = 66778 no. pairs analyzed = 66778 no. exposed pairs = 4053 no. arc points = 27911 no. surface atoms = 1363 nbur = 1942 mkacc time = 0.2300000 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= 199 mr = 3059 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 2966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2837 ## 402 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 7664 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8475488E-11 1.4744804E-11 midg,1,midg; midg,igrid,midg -5.1388255E-10 2.4848010E-10 1,midg,midg; igrid,midg,midg 2.4465700E-11 -6.8601839E-11 gauss-seidel spectral radius is 0.9811361 estimated iterations to convergence 60 setup time was (sec) 0.7800000 now iterating at: 17:49:38 rms-change max change #iterations 6.1726067E-02 18.63663 at 10iterations 3.6599846E-03 0.8306122 at 20iterations 2.4916377E-04 4.9177170E-02 at 30iterations 3.1623051E-05 6.2501431E-03 at 40iterations 6.9925768E-06 1.4111996E-03 at 50iterations finished qdiffx linear iterations at : 17:49:41 total time elapsed so far: 4.380000 # loops : 50 mean,max change (kT/e) : 6.9925768E-06 1.4111996E-03 energy calculations done at 4.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 17:49:42 4.611u 0.436s 0:05.31 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 Sat Oct 8 2011 at 17:49:42 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.566740 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): 41.21800 109.3850 ymin,ymax (A): 10.32300 56.99900 zmin,zma (A): 2.670000 51.21100 x,y,z range (A): 68.16701 46.67599 48.54100 scale (grids/A): 1.566740 object centre (A): 75.30150 33.66100 26.94050 number of atom coordinates read : 3305 total number of charged atoms : 3162 net assigned charge : -0.9999930 assigned positive charge : 499.5877 centred at (gu) : 90.79516 86.62725 90.70329 assigned negative charge : -500.5891 centred at (gu) : 90.84144 86.26487 90.67023 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 65254 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27911 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 19853 mr = 45360 m= 1775 mr = 13424 m= 47 mr = 729 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 619 time to turn everything in is 0.6600000 number of dielectric boundary points 27414 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 362 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 23962 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) : 0.5222468 object centre at (A) : 75.30150 33.66100 26.94050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1393846E-03 -2.8595293E-04 midg,1,midg; midg,igrid,midg -6.6106250E-03 4.8071076E-03 1,midg,midg; igrid,midg,midg 8.8927858E-03 -3.3106052E-03 gauss-seidel spectral radius is 0.9980476 estimated iterations to convergence 180 setup time was (sec) 0.9800000 now iterating at: 17:49:43 rms-change max change #iterations 3.244472 146.9559 at 10iterations 1.307664 61.03546 at 20iterations 0.5279629 21.13750 at 30iterations 0.2138891 8.181320 at 40iterations 8.6660609E-02 3.067211 at 50iterations 3.4890782E-02 1.243268 at 60iterations 1.4168654E-02 0.5379653 at 70iterations 5.7203989E-03 0.2043225 at 80iterations 2.3256717E-03 8.3843231E-02 at 90iterations 9.4557228E-04 4.0346146E-02 at 100iterations 3.9064011E-04 1.4813423E-02 at 110iterations 1.6378025E-04 6.4280033E-03 at 120iterations finished qdiffx linear iterations at : 17:49:52 total time elapsed so far: 9.820000 # loops : 120 mean,max change (kT/e) : 1.6378025E-04 6.4280033E-03 energy calculations done at 9.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.03000 DelPhi exited at 17:49:53 10.030u 0.483s 0:10.86 96.7% 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 Sat Oct 8 2011 at 17:49:53 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3305 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.350111 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): 41.21800 109.3850 ymin,ymax (A): 10.32300 56.99900 zmin,zma (A): 2.670000 51.21100 x,y,z range (A): 68.16701 46.67599 48.54100 scale (grids/A): 2.350111 object centre (A): 75.30150 33.66100 26.94050 number of atom coordinates read : 3305 total number of charged atoms : 3162 net assigned charge : -0.9999930 assigned positive charge : 499.5877 centred at (gu) : 91.19264 84.94051 91.05475 assigned negative charge : -500.5891 centred at (gu) : 91.26208 84.39726 91.00523 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 151929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27911 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 70125 mr = 111073 m= 18674 mr = 55383 m= 2605 mr = 13537 m= 154 mr = 1508 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 1996 time to turn everything in is 1.630000 number of dielectric boundary points 61945 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 43 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 25250 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) : 1.566740 object centre at (A) : 75.30150 33.66100 26.94050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5255045E-02 -7.2392747E-03 midg,1,midg; midg,igrid,midg -9.8308250E-02 8.5699312E-02 1,midg,midg; igrid,midg,midg 0.4862995 -0.1180221 gauss-seidel spectral radius is 0.9990973 estimated iterations to convergence 263 setup time was (sec) 1.980000 now iterating at: 17:49:55 rms-change max change #iterations 8.517540 250.8366 at 10iterations 4.707448 113.1766 at 20iterations 2.590142 58.45977 at 30iterations 1.423344 37.65293 at 40iterations 0.7771007 17.08823 at 50iterations 0.4239441 10.12991 at 60iterations 0.2312064 4.731987 at 70iterations 0.1255511 2.544353 at 80iterations 6.8203285E-02 1.382599 at 90iterations 3.7038933E-02 0.8013639 at 100iterations 2.0088950E-02 0.4051561 at 110iterations 1.0916984E-02 0.2337646 at 120iterations 5.9232553E-03 0.1201439 at 130iterations 3.2182888E-03 7.2469711E-02 at 140iterations 1.7416879E-03 3.8557053E-02 at 150iterations 9.4422163E-04 2.2546768E-02 at 160iterations 5.1236723E-04 1.1455536E-02 at 170iterations 2.7883158E-04 5.9671402E-03 at 180iterations finished qdiffx linear iterations at : 17:50:10 total time elapsed so far: 16.58000 # loops : 180 mean,max change (kT/e) : 2.7883158E-04 5.9671402E-03 energy calculations done at 16.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.81000 DelPhi exited at 17:50:10 16.814u 0.487s 0:17.57 98.4% 0+0k 0+0io 0pf+0w