Sun Oct 9 07:40:50 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+sph.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 = amb.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 07:40:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7384513 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): 3.976000 48.90800 ymin,ymax (A): 21.61800 69.82700 zmin,zma (A): -7.694000 35.65800 x,y,z range (A): 44.93200 48.20900 43.35200 scale (grids/A): 0.7384513 object centre (A): 26.44200 45.72250 13.98200 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 240.0202 centred at (gu) : 90.63014 88.95235 89.32291 assigned negative charge : -249.5201 centred at (gu) : 90.66502 88.69477 89.69188 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6093 nv = 96 ne = 84 npr = 34881 no. pairs analyzed = 34881 no. exposed pairs = 2118 no. arc points = 15019 no. surface atoms = 718 nbur = 931 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 424 mr = 3310 m= 1 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.2500000 number of dielectric boundary points 3125 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1232 ## 80 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 6409 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2951750E-07 -3.9922989E-07 midg,1,midg; midg,igrid,midg -4.4185529E-07 2.4656520E-08 1,midg,midg; igrid,midg,midg -1.1964420E-07 -2.1007696E-07 gauss-seidel spectral radius is 0.9903974 estimated iterations to convergence 83 setup time was (sec) 0.5300000 now iterating at: 07:40:51 rms-change max change #iterations 0.2064625 39.17723 at 10iterations 2.7541731E-02 4.024185 at 20iterations 3.6851016E-03 0.5062313 at 30iterations 4.8688921E-04 7.9002380E-02 at 40iterations 6.6030021E-05 8.6059570E-03 at 50iterations finished qdiffx linear iterations at : 07:40:54 total time elapsed so far: 3.800000 # loops : 50 mean,max change (kT/e) : 6.6030021E-05 8.6059570E-03 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.980000 DelPhi exited at 07:40:55 3.981u 0.261s 0:04.50 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 Sun Oct 9 2011 at 07:40:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.215354 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): 3.976000 48.90800 ymin,ymax (A): 21.61800 69.82700 zmin,zma (A): -7.694000 35.65800 x,y,z range (A): 44.93200 48.20900 43.35200 scale (grids/A): 2.215354 object centre (A): 26.44200 45.72250 13.98200 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 240.0202 centred at (gu) : 91.89060 86.85713 87.96896 assigned negative charge : -249.5201 centred at (gu) : 91.99521 86.08449 89.07575 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 63220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15019 grid for indexing accessible points = 1.400000 m= 26010 mr = 42494 m= 5888 mr = 19896 m= 602 mr = 4311 m= 11 mr = 314 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1251 time to turn everything in is 0.6000000 number of dielectric boundary points 28716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 12037 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) : 0.7384513 object centre at (A) : 26.44200 45.72250 13.98200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.2677129E-02 -8.9572281E-02 midg,1,midg; midg,igrid,midg -9.3816049E-02 4.2245455E-02 1,midg,midg; igrid,midg,midg -6.0262743E-02 -7.0208386E-02 gauss-seidel spectral radius is 0.9988798 estimated iterations to convergence 236 setup time was (sec) 0.9000000 now iterating at: 07:40:56 rms-change max change #iterations 4.382880 182.1347 at 10iterations 2.195256 81.44220 at 20iterations 1.104086 34.24697 at 30iterations 0.5534635 19.38563 at 40iterations 0.2773171 9.623857 at 50iterations 0.1396217 4.690335 at 60iterations 7.0032939E-02 2.384655 at 70iterations 3.5301130E-02 1.093048 at 80iterations 1.7699929E-02 0.5676050 at 90iterations 8.9090364E-03 0.2997589 at 100iterations 4.4614519E-03 0.1481190 at 110iterations 2.2469971E-03 6.5940857E-02 at 120iterations finished qdiffx linear iterations at : 07:41:04 total time elapsed so far: 9.100000 # loops : 120 mean,max change (kT/e) : 2.2469971E-03 6.5940857E-02 energy calculations done at 9.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.280000 DelPhi exited at 07:41:05 9.285u 0.289s 0:09.88 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 Sun Oct 9 2011 at 07:41:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1649 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.323031 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): 3.976000 48.90800 ymin,ymax (A): 21.61800 69.82700 zmin,zma (A): -7.694000 35.65800 x,y,z range (A): 44.93200 48.20900 43.35200 scale (grids/A): 3.323031 object centre (A): 26.44200 45.72250 13.98200 number of atom coordinates read : 1649 total number of charged atoms : 1512 net assigned charge : -9.499993 assigned positive charge : 240.0202 centred at (gu) : 92.83589 85.28579 86.95346 assigned negative charge : -249.5201 centred at (gu) : 92.99279 84.12680 88.61369 start vw surface at 0.1300000 fill in re-entrant regions at 0.8800000 boundary points on vw surface= 145274 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15019 grid for indexing accessible points = 1.400000 m= 77800 mr = 102249 m= 34901 mr = 64333 m= 11488 mr = 29510 m= 2428 mr = 9436 m= 324 mr = 1880 m= 14 mr = 210 m= 0 mr = 2 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 4521 time to turn everything in is 1.940000 number of dielectric boundary points 64609 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 12096 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) : 2.215354 object centre at (A) : 26.44200 45.72250 13.98200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3871706 -0.6586221 midg,1,midg; midg,igrid,midg -0.8079324 0.5620431 1,midg,midg; igrid,midg,midg -0.4165061 -0.5254663 gauss-seidel spectral radius is 0.9993048 estimated iterations to convergence 299 setup time was (sec) 2.250000 now iterating at: 07:41:07 rms-change max change #iterations 9.581083 327.3310 at 10iterations 5.610082 116.4434 at 20iterations 3.272660 64.30005 at 30iterations 1.909389 37.77821 at 40iterations 1.114392 20.41587 at 50iterations 0.6510053 11.66827 at 60iterations 0.3798295 7.208427 at 70iterations 0.2213933 4.147734 at 80iterations 0.1292630 2.415781 at 90iterations 7.5482748E-02 1.314479 at 100iterations 4.3920301E-02 0.7899561 at 110iterations 2.5627578E-02 0.4471273 at 120iterations 1.4959195E-02 0.2607255 at 130iterations 8.7410295E-03 0.1659813 at 140iterations 5.1030167E-03 9.2151642E-02 at 150iterations 2.9726450E-03 5.0789356E-02 at 160iterations 1.7369968E-03 3.0955315E-02 at 170iterations 1.0124878E-03 1.8142700E-02 at 180iterations finished qdiffx linear iterations at : 07:41:21 total time elapsed so far: 15.58000 # loops : 180 mean,max change (kT/e) : 1.0124878E-03 1.8142700E-02 energy calculations done at 15.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.75000 DelPhi exited at 07:41:21 15.756u 0.310s 0:16.36 98.1% 0+0k 0+0io 0pf+0w