Tue Oct 11 03:16:29 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 03:16:29 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3199 !!! WARNING: GLM 12 has a net charge of -0.0940 !!! WARNING: SEP 223 has a net charge of -0.4750 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: 0.5346550 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): -3.236000 56.30600 ymin,ymax (A): 35.90900 102.4940 zmin,zma (A): 60.16300 110.3530 x,y,z range (A): 59.54200 66.58500 50.19000 scale (grids/A): 0.5346550 object centre (A): 26.53500 69.20149 85.25800 number of atom coordinates read : 3199 total number of charged atoms : 3054 net assigned charge : -6.568974 assigned positive charge : 480.8108 centred at (gu) : 91.50390 92.91402 88.93491 assigned negative charge : -487.3808 centred at (gu) : 91.48897 92.94151 88.98220 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 5711 nv = 96 ne = 84 npr = 66459 no. pairs analyzed = 66459 no. exposed pairs = 3978 no. arc points = 27194 no. surface atoms = 1346 nbur = 1853 mkacc time = 0.1100000 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 = 1.596000 m= 222 mr = 2990 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 2935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2757 ## 410 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 7662 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4584968E-11 -3.6605766E-10 midg,1,midg; midg,igrid,midg -6.5651942E-11 -8.0336243E-10 1,midg,midg; igrid,midg,midg -2.2502065E-10 -2.6842251E-10 gauss-seidel spectral radius is 0.9819825 estimated iterations to convergence 61 setup time was (sec) 0.4400000 now iterating at: 03:16:30 rms-change max change #iterations 7.2231390E-02 12.36664 at 10iterations 4.6220575E-03 0.8231659 at 20iterations 4.2654455E-04 8.0929339E-02 at 30iterations 8.3394945E-05 2.0320654E-02 at 40iterations 2.2544315E-05 5.5711269E-03 at 50iterations finished qdiffx linear iterations at : 03:16:32 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 2.2544315E-05 5.5711269E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 03:16:33 3.448u 0.156s 0:03.93 91.3% 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 03:16:33 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3199 !!! WARNING: GLM 12 has a net charge of -0.0940 !!! WARNING: SEP 223 has a net charge of -0.4750 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: 1.603965 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): -3.236000 56.30600 ymin,ymax (A): 35.90900 102.4940 zmin,zma (A): 60.16300 110.3530 x,y,z range (A): 59.54200 66.58500 50.19000 scale (grids/A): 1.603965 object centre (A): 26.53500 69.20149 85.25800 number of atom coordinates read : 3199 total number of charged atoms : 3054 net assigned charge : -6.568974 assigned positive charge : 480.8108 centred at (gu) : 94.51111 98.74104 86.80376 assigned negative charge : -487.3808 centred at (gu) : 94.46664 98.82451 86.94637 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 63462 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27194 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 18984 mr = 42884 m= 1872 mr = 13116 m= 43 mr = 835 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 143 time to turn everything in is 0.3200000 number of dielectric boundary points 27527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 349 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 23265 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) : 0.5346550 object centre at (A) : 26.53500 69.20149 85.25800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.7777757E-03 -6.8188477E-03 midg,1,midg; midg,igrid,midg 2.2386497E-02 -1.4808006E-02 1,midg,midg; igrid,midg,midg -3.8073242E-03 5.4558082E-03 gauss-seidel spectral radius is 0.9981210 estimated iterations to convergence 183 setup time was (sec) 0.5400000 now iterating at: 03:16:34 rms-change max change #iterations 3.342412 152.3938 at 10iterations 1.371803 57.19207 at 20iterations 0.5615084 21.58943 at 30iterations 0.2309081 8.540383 at 40iterations 9.4869688E-02 3.874903 at 50iterations 3.9023679E-02 1.494373 at 60iterations 1.6075965E-02 0.6254869 at 70iterations 6.6128010E-03 0.2581577 at 80iterations 2.7624350E-03 9.8512650E-02 at 90iterations 1.1577257E-03 4.0799499E-02 at 100iterations 5.0312770E-04 1.9815564E-02 at 110iterations 2.2895930E-04 1.0546923E-02 at 120iterations finished qdiffx linear iterations at : 03:16:41 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 2.2895930E-04 1.0546923E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 03:16:41 7.651u 0.196s 0:08.23 95.2% 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 Tue Oct 11 2011 at 03:16:41 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3199 !!! WARNING: GLM 12 has a net charge of -0.0940 !!! WARNING: SEP 223 has a net charge of -0.4750 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: 2.405947 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): -3.236000 56.30600 ymin,ymax (A): 35.90900 102.4940 zmin,zma (A): 60.16300 110.3530 x,y,z range (A): 59.54200 66.58500 50.19000 scale (grids/A): 2.405947 object centre (A): 26.53500 69.20149 85.25800 number of atom coordinates read : 3199 total number of charged atoms : 3054 net assigned charge : -6.568974 assigned positive charge : 480.8108 centred at (gu) : 96.76647 103.1115 85.20543 assigned negative charge : -487.3808 centred at (gu) : 96.69979 103.2367 85.41933 start vw surface at 0.1000000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 147683 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27194 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 66481 mr = 105425 m= 18405 mr = 52413 m= 2764 mr = 13676 m= 176 mr = 1679 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 493 time to turn everything in is 0.7800000 number of dielectric boundary points 62250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 26 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 24389 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) : 1.603965 object centre at (A) : 26.53500 69.20149 85.25800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5016341E-02 -9.6160397E-02 midg,1,midg; midg,igrid,midg 0.4100152 -0.3837109 1,midg,midg; igrid,midg,midg -7.3741018E-03 0.1786512 gauss-seidel spectral radius is 0.9991171 estimated iterations to convergence 266 setup time was (sec) 1.010000 now iterating at: 03:16:42 rms-change max change #iterations 8.770557 340.6739 at 10iterations 4.904093 121.2529 at 20iterations 2.722408 63.78411 at 30iterations 1.509015 36.36531 at 40iterations 0.8308495 17.82866 at 50iterations 0.4554947 10.77462 at 60iterations 0.2503842 5.326995 at 70iterations 0.1370431 3.450915 at 80iterations 7.4950241E-02 1.541675 at 90iterations 4.1023038E-02 0.8252368 at 100iterations 2.2390731E-02 0.4982681 at 110iterations 1.2283819E-02 0.2715759 at 120iterations 6.7170556E-03 0.1412468 at 130iterations 3.6788348E-03 7.2563171E-02 at 140iterations 2.0194440E-03 4.0439606E-02 at 150iterations 1.1160094E-03 2.4083614E-02 at 160iterations 6.2636787E-04 1.4775276E-02 at 170iterations 3.5780552E-04 8.4719658E-03 at 180iterations finished qdiffx linear iterations at : 03:16:54 total time elapsed so far: 12.10000 # loops : 180 mean,max change (kT/e) : 3.5780552E-04 8.4719658E-03 energy calculations done at 12.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.23000 DelPhi exited at 03:16:54 12.234u 0.204s 0:12.77 97.3% 0+0k 0+0io 0pf+0w