Tue Oct 11 03:35:05 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 Tue Oct 11 2011 at 03:35:05 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2186 !!! WARNING: GLU 460 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6115683 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): -15.56700 26.99000 ymin,ymax (A): -2.479000 51.40600 zmin,zma (A): -5.068000 53.14300 x,y,z range (A): 42.55700 53.88500 58.21100 scale (grids/A): 0.6115683 object centre (A): 5.711500 24.46350 24.03750 number of atom coordinates read : 2186 total number of charged atoms : 2088 net assigned charge : -6.499980 assigned positive charge : 320.3914 centred at (gu) : 89.16103 89.43907 89.10388 assigned negative charge : -326.8919 centred at (gu) : 89.00026 89.54739 89.12868 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5525 nv = 96 ne = 84 npr = 44636 no. pairs analyzed = 44636 no. exposed pairs = 2761 no. arc points = 19782 no. surface atoms = 938 nbur = 1248 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 267 mr = 2951 m= 0 mr = 19 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1879 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6712 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5206653E-09 -4.1780286E-09 midg,1,midg; midg,igrid,midg 7.9979712E-10 -7.7488114E-09 1,midg,midg; igrid,midg,midg -1.3437434E-08 2.3634830E-09 gauss-seidel spectral radius is 0.9861267 estimated iterations to convergence 70 setup time was (sec) 0.4700000 now iterating at: 03:35:06 rms-change max change #iterations 0.1080956 17.79701 at 10iterations 9.5047317E-03 1.487385 at 20iterations 8.5290585E-04 0.1428986 at 30iterations 7.3935887E-05 1.1428833E-02 at 40iterations 6.6362177E-06 1.0366440E-03 at 50iterations finished qdiffx linear iterations at : 03:35:09 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 6.6362177E-06 1.0366440E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.100000 DelPhi exited at 03:35:09 3.102u 0.135s 0:03.56 90.7% 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 03:35:09 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2186 !!! WARNING: GLU 460 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.834705 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): -15.56700 26.99000 ymin,ymax (A): -2.479000 51.40600 zmin,zma (A): -5.068000 53.14300 x,y,z range (A): 42.55700 53.88500 58.21100 scale (grids/A): 1.834705 object centre (A): 5.711500 24.46350 24.03750 number of atom coordinates read : 2186 total number of charged atoms : 2088 net assigned charge : -6.499980 assigned positive charge : 320.3914 centred at (gu) : 87.48270 88.31693 87.31155 assigned negative charge : -326.8919 centred at (gu) : 87.00082 88.64208 87.38589 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 59834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19782 grid for indexing accessible points = 1.400000 m= 19789 mr = 40584 m= 2759 mr = 14241 m= 109 mr = 1589 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4600000 number of dielectric boundary points 26054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 16354 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) : 0.6115683 object centre at (A) : 5.711500 24.46350 24.03750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1792939E-03 -2.4190251E-02 midg,1,midg; midg,igrid,midg -3.7843380E-02 -3.8838632E-02 1,midg,midg; igrid,midg,midg -9.7570531E-03 1.6562603E-02 gauss-seidel spectral radius is 0.9984916 estimated iterations to convergence 204 setup time was (sec) 0.7300000 now iterating at: 03:35:10 rms-change max change #iterations 3.555488 170.6176 at 10iterations 1.593965 64.95725 at 20iterations 0.7189043 29.27336 at 30iterations 0.3236215 12.21962 at 40iterations 0.1456933 5.121367 at 50iterations 6.5734491E-02 2.673611 at 60iterations 2.9490568E-02 1.065878 at 70iterations 1.3281368E-02 0.4697483 at 80iterations 6.0067284E-03 0.2148902 at 90iterations 2.6871017E-03 9.6907616E-02 at 100iterations 1.2128577E-03 4.2934418E-02 at 110iterations 5.4685317E-04 2.0863533E-02 at 120iterations finished qdiffx linear iterations at : 03:35:16 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 5.4685317E-04 2.0863533E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 03:35:17 6.997u 0.211s 0:07.51 95.8% 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 Tue Oct 11 2011 at 03:35:17 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2186 !!! WARNING: GLU 460 has a net charge of -2.0000 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: 2.752057 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): -15.56700 26.99000 ymin,ymax (A): -2.479000 51.40600 zmin,zma (A): -5.068000 53.14300 x,y,z range (A): 42.55700 53.88500 58.21100 scale (grids/A): 2.752057 object centre (A): 5.711500 24.46350 24.03750 number of atom coordinates read : 2186 total number of charged atoms : 2088 net assigned charge : -6.499980 assigned positive charge : 320.3914 centred at (gu) : 86.22395 87.47523 85.96712 assigned negative charge : -326.8919 centred at (gu) : 85.50126 87.96314 86.07889 start vw surface at 0.1800000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 138736 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19782 grid for indexing accessible points = 1.400000 m= 65935 mr = 99130 m= 22306 mr = 53101 m= 4711 mr = 17496 m= 508 mr = 3415 m= 13 mr = 298 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.5699999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.060000 number of dielectric boundary points 58767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 16701 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) : 1.834705 object centre at (A) : 5.711500 24.46350 24.03750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1933870E-02 -0.3248261 midg,1,midg; midg,igrid,midg -0.4094590 -0.4761933 1,midg,midg; igrid,midg,midg -6.7369290E-02 0.2294874 gauss-seidel spectral radius is 0.9992155 estimated iterations to convergence 282 setup time was (sec) 1.330000 now iterating at: 03:35:18 rms-change max change #iterations 8.491108 276.5571 at 10iterations 4.834816 114.3371 at 20iterations 2.738362 62.80091 at 30iterations 1.545299 34.14903 at 40iterations 0.8749093 18.36958 at 50iterations 0.4922805 9.986539 at 60iterations 0.2783021 6.247317 at 70iterations 0.1566360 3.045543 at 80iterations 8.8303968E-02 1.997276 at 90iterations 4.9812697E-02 0.9594574 at 100iterations 2.8043970E-02 0.5349388 at 110iterations 1.5830504E-02 0.3323603 at 120iterations 8.9118453E-03 0.1919775 at 130iterations 5.0225388E-03 0.1042681 at 140iterations 2.8349692E-03 5.5173874E-02 at 150iterations 1.5968150E-03 3.5510063E-02 at 160iterations 8.9954573E-04 1.8316269E-02 at 170iterations 5.0895399E-04 1.0509491E-02 at 180iterations finished qdiffx linear iterations at : 03:35:28 total time elapsed so far: 11.43000 # loops : 180 mean,max change (kT/e) : 5.0895399E-04 1.0509491E-02 energy calculations done at 11.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.61000 DelPhi exited at 03:35:29 11.612u 0.208s 0:12.29 96.0% 0+0k 0+0io 0pf+0w