Tue Oct 11 07:33:33 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 07:33:33 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3264 !!! WARNING: GLM 58 has a net charge of -0.0940 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 0.5990140 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): 0.5429999 49.16300 ymin,ymax (A): -8.339000 49.48400 zmin,zma (A): 1.346000 60.77700 x,y,z range (A): 48.62000 57.82300 59.43100 scale (grids/A): 0.5990140 object centre (A): 24.85300 20.57250 31.06150 number of atom coordinates read : 3264 total number of charged atoms : 3089 net assigned charge : -0.6939893 assigned positive charge : 488.4059 centred at (gu) : 89.58670 89.40892 90.77147 assigned negative charge : -489.1009 centred at (gu) : 89.51817 89.35490 90.71721 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7710 nv = 96 ne = 84 npr = 67352 no. pairs analyzed = 67352 no. exposed pairs = 3918 no. arc points = 26301 no. surface atoms = 1341 nbur = 1923 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 364 mr = 4433 m= 1 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2640 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 9641 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2704614E-09 2.5485312E-09 midg,1,midg; midg,igrid,midg -3.0945659E-09 1.8447953E-09 1,midg,midg; igrid,midg,midg -3.6917596E-09 2.5020326E-09 gauss-seidel spectral radius is 0.9856262 estimated iterations to convergence 68 setup time was (sec) 0.6900000 now iterating at: 07:33:34 rms-change max change #iterations 0.1221345 18.59784 at 10iterations 1.2256033E-02 1.919224 at 20iterations 2.7673359E-03 0.4680672 at 30iterations 1.1018447E-03 0.1990242 at 40iterations 4.6635623E-04 8.4190369E-02 at 50iterations finished qdiffx linear iterations at : 07:33:37 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 4.6635623E-04 8.4190369E-02 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 07:33:37 4.214u 0.272s 0:04.83 92.7% 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 07:33:38 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3264 !!! WARNING: GLM 58 has a net charge of -0.0940 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 1.797042 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): 0.5429999 49.16300 ymin,ymax (A): -8.339000 49.48400 zmin,zma (A): 1.346000 60.77700 x,y,z range (A): 48.62000 57.82300 59.43100 scale (grids/A): 1.797042 object centre (A): 24.85300 20.57250 31.06150 number of atom coordinates read : 3264 total number of charged atoms : 3089 net assigned charge : -0.6939893 assigned positive charge : 488.4059 centred at (gu) : 88.75924 88.22627 92.31354 assigned negative charge : -489.1009 centred at (gu) : 88.55416 88.06435 92.15114 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 84875 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26301 grid for indexing accessible points = 1.400000 m= 30814 mr = 60813 m= 4127 mr = 23188 m= 144 mr = 2519 m= 0 mr = 34 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1199 time to turn everything in is 0.7400000 number of dielectric boundary points 33406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 189 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 24109 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) : 0.5990140 object centre at (A) : 24.85300 20.57250 31.06150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5211469E-02 -1.7148806E-03 midg,1,midg; midg,igrid,midg -1.3258813E-02 6.0592969E-03 1,midg,midg; igrid,midg,midg -6.8312045E-03 4.2243334E-03 gauss-seidel spectral radius is 0.9985331 estimated iterations to convergence 207 setup time was (sec) 1.050000 now iterating at: 07:33:39 rms-change max change #iterations 4.332188 162.2781 at 10iterations 1.973538 66.99531 at 20iterations 0.9009110 30.40186 at 30iterations 0.4130429 12.04166 at 40iterations 0.1891517 5.716557 at 50iterations 8.6807773E-02 2.444759 at 60iterations 4.0108066E-02 1.497276 at 70iterations 1.8962432E-02 0.6708984 at 80iterations 9.3991412E-03 0.3390007 at 90iterations 5.0432803E-03 0.1715508 at 100iterations 3.0294817E-03 0.1095619 at 110iterations 2.0249896E-03 7.7602386E-02 at 120iterations finished qdiffx linear iterations at : 07:33:47 total time elapsed so far: 9.580000 # loops : 120 mean,max change (kT/e) : 2.0249896E-03 7.7602386E-02 energy calculations done at 9.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.760000 DelPhi exited at 07:33:48 9.758u 0.315s 0:10.68 94.1% 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 07:33:48 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: 329 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3264 !!! WARNING: GLM 58 has a net charge of -0.0940 !!! WARNING: UMP 529 has a net charge of -0.1000 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: 2.695563 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): 0.5429999 49.16300 ymin,ymax (A): -8.339000 49.48400 zmin,zma (A): 1.346000 60.77700 x,y,z range (A): 48.62000 57.82300 59.43100 scale (grids/A): 2.695563 object centre (A): 24.85300 20.57250 31.06150 number of atom coordinates read : 3264 total number of charged atoms : 3089 net assigned charge : -0.6939893 assigned positive charge : 488.4059 centred at (gu) : 88.13852 87.33916 93.47018 assigned negative charge : -489.1009 centred at (gu) : 87.83104 87.09654 93.22685 start vw surface at 0.1800000 fill in re-entrant regions at 0.6300000 boundary points on vw surface= 196497 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26301 grid for indexing accessible points = 1.400000 m= 101587 mr = 146998 m= 35007 mr = 84241 m= 7251 mr = 28597 m= 680 mr = 5375 m= 20 mr = 406 m= 0 mr = 0 time to grow re-entrant surface = 1.170000 no. cavity mid-points inaccessible to solvent = 4005 time to turn everything in is 1.920000 number of dielectric boundary points 75425 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 24711 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) : 1.797042 object centre at (A) : 24.85300 20.57250 31.06150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4539213 -0.1541611 midg,1,midg; midg,igrid,midg -0.3247344 0.1230826 1,midg,midg; igrid,midg,midg -6.3016050E-02 2.9023321E-02 gauss-seidel spectral radius is 0.9992418 estimated iterations to convergence 287 setup time was (sec) 2.260000 now iterating at: 07:33:51 rms-change max change #iterations 10.46179 328.0670 at 10iterations 6.103801 146.0620 at 20iterations 3.527090 68.86835 at 30iterations 2.037861 51.35705 at 40iterations 1.177133 25.18718 at 50iterations 0.6754023 12.01825 at 60iterations 0.3879905 6.885090 at 70iterations 0.2225353 4.029858 at 80iterations 0.1275240 2.158017 at 90iterations 7.3004916E-02 1.265096 at 100iterations 4.1901287E-02 0.7276430 at 110iterations 2.4059014E-02 0.4319782 at 120iterations 1.3929618E-02 0.2581596 at 130iterations 8.1473850E-03 0.1560509 at 140iterations 4.8774816E-03 0.1018677 at 150iterations 3.0480123E-03 6.9530487E-02 at 160iterations 2.0313952E-03 4.1358948E-02 at 170iterations 1.4549781E-03 3.2199860E-02 at 180iterations finished qdiffx linear iterations at : 07:34:05 total time elapsed so far: 16.51000 # loops : 180 mean,max change (kT/e) : 1.4549781E-03 3.2199860E-02 energy calculations done at 16.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.69000 DelPhi exited at 07:34:06 16.693u 0.325s 0:17.73 95.9% 0+0k 0+0io 0pf+0w