Sat Oct 8 15:57:04 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 15:57:04 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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: 0.5834248 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): -2.185000 45.48900 ymin,ymax (A): -15.37300 30.06200 zmin,zma (A): -19.26100 41.75800 x,y,z range (A): 47.67400 45.43500 61.01900 scale (grids/A): 0.5834248 object centre (A): 21.65200 7.344501 11.24850 number of atom coordinates read : 2358 total number of charged atoms : 2265 net assigned charge : 2.806003 assigned positive charge : 351.4631 centred at (gu) : 90.56072 88.58472 88.89549 assigned negative charge : -348.6577 centred at (gu) : 90.57071 88.73330 88.94739 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5189 nv = 96 ne = 84 npr = 48464 no. pairs analyzed = 48464 no. exposed pairs = 2914 no. arc points = 20314 no. surface atoms = 1000 nbur = 1358 mkacc time = 0.1300000 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 = 1.484000 m= 222 mr = 2754 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3100000 number of dielectric boundary points 2647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2094 ## 234 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 6730 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1068871E-09 -2.8043640E-10 midg,1,midg; midg,igrid,midg 4.8190771E-09 -1.6264936E-09 1,midg,midg; igrid,midg,midg 7.2721751E-10 4.9852633E-10 gauss-seidel spectral radius is 0.9847810 estimated iterations to convergence 67 setup time was (sec) 0.5700000 now iterating at: 15:57:05 rms-change max change #iterations 9.0222888E-02 15.45336 at 10iterations 7.1489383E-03 1.203424 at 20iterations 5.9748808E-04 9.3502045E-02 at 30iterations 6.7005778E-05 1.0613102E-02 at 40iterations 1.2334353E-05 2.2015572E-03 at 50iterations finished qdiffx linear iterations at : 15:57:08 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 1.2334353E-05 2.2015572E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 15:57:09 4.021u 0.270s 0:04.57 93.8% 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 15:57:09 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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: 1.750274 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): -2.185000 45.48900 ymin,ymax (A): -15.37300 30.06200 zmin,zma (A): -19.26100 41.75800 x,y,z range (A): 47.67400 45.43500 61.01900 scale (grids/A): 1.750274 object centre (A): 21.65200 7.344501 11.24850 number of atom coordinates read : 2358 total number of charged atoms : 2265 net assigned charge : 2.806003 assigned positive charge : 351.4631 centred at (gu) : 91.68185 85.75372 86.68601 assigned negative charge : -348.6577 centred at (gu) : 91.71199 86.19970 86.84201 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 57384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20314 grid for indexing accessible points = 1.400000 m= 18236 mr = 39267 m= 2226 mr = 12883 m= 71 mr = 1297 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1057 time to turn everything in is 0.5200000 number of dielectric boundary points 24455 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 17641 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) : 0.5834248 object centre at (A) : 21.65200 7.344501 11.24850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5761372E-02 1.1478839E-02 midg,1,midg; midg,igrid,midg 1.4614491E-02 -3.9220289E-03 1,midg,midg; igrid,midg,midg 1.7453226E-03 -1.6042417E-02 gauss-seidel spectral radius is 0.9983563 estimated iterations to convergence 196 setup time was (sec) 0.8100000 now iterating at: 15:57:10 rms-change max change #iterations 3.376251 183.8691 at 10iterations 1.472488 56.29027 at 20iterations 0.6426049 23.61455 at 30iterations 0.2794698 10.35043 at 40iterations 0.1224288 4.503342 at 50iterations 5.3109892E-02 1.850815 at 60iterations 2.3178644E-02 0.8897781 at 70iterations 1.0111196E-02 0.3859944 at 80iterations 4.4022170E-03 0.1572876 at 90iterations 1.9263610E-03 6.7430496E-02 at 100iterations 8.3781616E-04 3.1994820E-02 at 110iterations 3.6781619E-04 1.4781952E-02 at 120iterations finished qdiffx linear iterations at : 15:57:18 total time elapsed so far: 8.920000 # loops : 120 mean,max change (kT/e) : 3.6781619E-04 1.4781952E-02 energy calculations done at 8.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.090000 DelPhi exited at 15:57:19 9.095u 0.292s 0:09.69 96.8% 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 15:57:19 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2358 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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: 2.625412 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): -2.185000 45.48900 ymin,ymax (A): -15.37300 30.06200 zmin,zma (A): -19.26100 41.75800 x,y,z range (A): 47.67400 45.43500 61.01900 scale (grids/A): 2.625412 object centre (A): 21.65200 7.344501 11.24850 number of atom coordinates read : 2358 total number of charged atoms : 2265 net assigned charge : 2.806003 assigned positive charge : 351.4631 centred at (gu) : 92.52277 83.63040 85.02888 assigned negative charge : -348.6577 centred at (gu) : 92.56793 84.29950 85.26299 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 133155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20314 grid for indexing accessible points = 1.400000 m= 61643 mr = 95841 m= 19384 mr = 49172 m= 3847 mr = 15217 m= 328 mr = 2776 m= 12 mr = 195 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 3583 time to turn everything in is 1.270000 number of dielectric boundary points 55168 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 18117 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) : 1.750274 object centre at (A) : 21.65200 7.344501 11.24850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2102840 0.3809240 midg,1,midg; midg,igrid,midg 0.1639571 -5.5287268E-02 1,midg,midg; igrid,midg,midg 3.7379790E-02 -0.2760350 gauss-seidel spectral radius is 0.9991742 estimated iterations to convergence 275 setup time was (sec) 1.580000 now iterating at: 15:57:21 rms-change max change #iterations 8.369541 293.2953 at 10iterations 4.764350 113.0511 at 20iterations 2.687348 63.31830 at 30iterations 1.513569 45.13091 at 40iterations 0.8516847 18.36202 at 50iterations 0.4791553 10.27948 at 60iterations 0.2678887 6.382620 at 70iterations 0.1498081 3.330171 at 80iterations 8.3750993E-02 1.811863 at 90iterations 4.6752457E-02 1.045151 at 100iterations 2.6112605E-02 0.5857239 at 110iterations 1.4597661E-02 0.2924494 at 120iterations 8.1469277E-03 0.1740631 at 130iterations 4.5382748E-03 9.0626717E-02 at 140iterations 2.5315902E-03 5.1309586E-02 at 150iterations 1.4117151E-03 2.9060960E-02 at 160iterations 7.8845921E-04 1.8021584E-02 at 170iterations 4.4119864E-04 9.3688965E-03 at 180iterations finished qdiffx linear iterations at : 15:57:34 total time elapsed so far: 14.67000 # loops : 180 mean,max change (kT/e) : 4.4119864E-04 9.3688965E-03 energy calculations done at 14.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.84000 DelPhi exited at 15:57:34 14.842u 0.313s 0:15.44 98.1% 0+0k 0+0io 0pf+0w