Wed Feb 15 08:56:33 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:33 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 ! Automatically converted by prot2crg.py # of charge parameter records: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3813 !!! WARNING: DIC 170 has a net charge of -0.8000 !!! WARNING: HIY 172 has a net charge of 0.2000 !!! WARNING: DIC 258 has a net charge of -0.8000 !!! WARNING: ZN 1098 has a net charge of 1.4000 !!! WARNING: CA 1099 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5712451 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): 32.59500 94.91500 ymin,ymax (A): -2.061000 56.44800 zmin,zma (A): -32.60900 27.25900 x,y,z range (A): 62.32000 58.50900 59.86800 scale (grids/A): 0.5712451 object centre (A): 63.75500 27.19350 -2.675000 number of atom coordinates read : 3813 total number of charged atoms : 3673 net assigned charge : 5.000020 assigned positive charge : 585.3239 centred at (gu) : 88.21684 89.61327 90.38301 assigned negative charge : -580.3262 centred at (gu) : 88.31611 89.67448 90.44369 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7871 nv = 96 ne = 84 npr = 79255 no. pairs analyzed = 79255 no. exposed pairs = 4402 no. arc points = 30345 no. surface atoms = 1490 nbur = 2323 mkacc time = 0.2200000 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 = 1.512000 m= 328 mr = 4453 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.5000000 number of dielectric boundary points 3723 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3194 ## 412 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 10400 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8664177E-09 -6.0299782E-10 midg,1,midg; midg,igrid,midg 2.2521804E-09 -5.0432142E-10 1,midg,midg; igrid,midg,midg 4.3815458E-09 -8.9321583E-10 gauss-seidel spectral radius is 0.9842399 estimated iterations to convergence 65 setup time was (sec) 0.7700000 now iterating at: 08:56:35 rms-change max change #iterations 0.1044893 14.46483 at 10iterations 7.9602981E-03 1.027559 at 20iterations 6.8044348E-04 0.1115913 at 30iterations 1.1536278E-04 1.6094374E-02 at 40iterations 3.3554257E-05 5.3099394E-03 at 50iterations finished qdiffx linear iterations at : 08:56:38 total time elapsed so far: 4.060000 # loops : 50 mean,max change (kT/e) : 3.3554257E-05 5.3099394E-03 energy calculations done at 4.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.240000 DelPhi exited at 08:56:38 4.242u 0.351s 0:04.93 93.1% 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 Wed Feb 15 2012 at 08:56:38 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 ! Automatically converted by prot2crg.py # of charge parameter records: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3813 !!! WARNING: DIC 170 has a net charge of -0.8000 !!! WARNING: HIY 172 has a net charge of 0.2000 !!! WARNING: DIC 258 has a net charge of -0.8000 !!! WARNING: ZN 1098 has a net charge of 1.4000 !!! WARNING: CA 1099 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.713735 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): 32.59500 94.91500 ymin,ymax (A): -2.061000 56.44800 zmin,zma (A): -32.60900 27.25900 x,y,z range (A): 62.32000 58.50900 59.86800 scale (grids/A): 1.713735 object centre (A): 63.75500 27.19350 -2.675000 number of atom coordinates read : 3813 total number of charged atoms : 3673 net assigned charge : 5.000020 assigned positive charge : 585.3239 centred at (gu) : 84.64906 88.83860 91.14748 assigned negative charge : -580.3262 centred at (gu) : 84.94781 89.02290 91.33069 start vw surface at 0.2000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 87940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30345 grid for indexing accessible points = 1.400000 m= 27594 mr = 62822 m= 3072 mr = 19959 m= 93 mr = 1666 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1467 time to turn everything in is 0.7600000 number of dielectric boundary points 34237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 324 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 28406 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) : 0.5712451 object centre at (A) : 63.75500 27.19350 -2.675000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3436170E-02 -1.5462472E-02 midg,1,midg; midg,igrid,midg 2.1966608E-02 9.3521196E-03 1,midg,midg; igrid,midg,midg 2.5053961E-02 -9.4367815E-03 gauss-seidel spectral radius is 0.9984189 estimated iterations to convergence 200 setup time was (sec) 1.060000 now iterating at: 08:56:40 rms-change max change #iterations 4.315479 163.0658 at 10iterations 1.904224 61.88780 at 20iterations 0.8418496 25.85452 at 30iterations 0.3732467 12.17792 at 40iterations 0.1651389 5.379166 at 50iterations 7.3164865E-02 2.630383 at 60iterations 3.2381400E-02 1.021166 at 70iterations 1.4357449E-02 0.4251633 at 80iterations 6.3882242E-03 0.1859388 at 90iterations 2.8585542E-03 9.1381073E-02 at 100iterations 1.2853901E-03 3.7368774E-02 at 110iterations 5.8652036E-04 1.7383575E-02 at 120iterations finished qdiffx linear iterations at : 08:56:48 total time elapsed so far: 9.430000 # loops : 120 mean,max change (kT/e) : 5.8652036E-04 1.7383575E-02 energy calculations done at 9.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.600000 DelPhi exited at 08:56:49 9.600u 0.285s 0:10.39 95.0% 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 Wed Feb 15 2012 at 08:56:49 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 ! Automatically converted by prot2crg.py # of charge parameter records: 963 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3813 !!! WARNING: DIC 170 has a net charge of -0.8000 !!! WARNING: HIY 172 has a net charge of 0.2000 !!! WARNING: DIC 258 has a net charge of -0.8000 !!! WARNING: ZN 1098 has a net charge of 1.4000 !!! WARNING: CA 1099 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.570603 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): 32.59500 94.91500 ymin,ymax (A): -2.061000 56.44800 zmin,zma (A): -32.60900 27.25900 x,y,z range (A): 62.32000 58.50900 59.86800 scale (grids/A): 2.570603 object centre (A): 63.75500 27.19350 -2.675000 number of atom coordinates read : 3813 total number of charged atoms : 3673 net assigned charge : 5.000020 assigned positive charge : 585.3239 centred at (gu) : 81.97343 88.25751 91.72104 assigned negative charge : -580.3262 centred at (gu) : 82.42160 88.53419 91.99583 start vw surface at 0.2100000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 204983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30345 grid for indexing accessible points = 1.400000 m= 96186 mr = 153218 m= 27789 mr = 78407 m= 4965 mr = 21771 m= 426 mr = 3508 m= 11 mr = 238 m= 0 mr = 4 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 4574 time to turn everything in is 1.890000 number of dielectric boundary points 77214 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 29374 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) : 1.713735 object centre at (A) : 63.75500 27.19350 -2.675000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8971753 -0.3020765 midg,1,midg; midg,igrid,midg 0.3639552 0.1401121 1,midg,midg; igrid,midg,midg 3.4996167E-02 -0.1169278 gauss-seidel spectral radius is 0.9992134 estimated iterations to convergence 281 setup time was (sec) 2.220000 now iterating at: 08:56:51 rms-change max change #iterations 10.55978 392.5789 at 10iterations 6.033689 154.2602 at 20iterations 3.444823 83.94740 at 30iterations 1.961468 45.51971 at 40iterations 1.113541 20.58794 at 50iterations 0.6327500 11.41656 at 60iterations 0.3584341 6.709841 at 70iterations 0.2027905 3.991406 at 80iterations 0.1149237 2.072472 at 90iterations 6.4848587E-02 1.097382 at 100iterations 3.6766157E-02 0.6945496 at 110iterations 2.0801052E-02 0.3945885 at 120iterations 1.1766180E-02 0.2126675 at 130iterations 6.6642561E-03 0.1184616 at 140iterations 3.7894722E-03 6.7127228E-02 at 150iterations 2.1608740E-03 3.7464142E-02 at 160iterations 1.2401526E-03 2.3222446E-02 at 170iterations 7.2291063E-04 1.2825012E-02 at 180iterations finished qdiffx linear iterations at : 08:57:05 total time elapsed so far: 16.04000 # loops : 180 mean,max change (kT/e) : 7.2291063E-04 1.2825012E-02 energy calculations done at 16.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.21000 DelPhi exited at 08:57:06 16.216u 0.302s 0:16.85 97.9% 0+0k 0+0io 0pf+0w