Sat Oct 15 15:06:45 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 Sat Oct 15 2011 at 15:06:45 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1158 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7490321 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): -6.573000 32.12200 ymin,ymax (A): 0.8600000 39.64800 zmin,zma (A): -1.496000 46.03200 x,y,z range (A): 38.69500 38.78800 47.52800 scale (grids/A): 0.7490321 object centre (A): 12.77450 20.25400 22.26800 number of atom coordinates read : 1158 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 88.66641 89.42522 88.39725 assigned negative charge : -169.8232 centred at (gu) : 88.37080 89.39206 88.45231 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 4446 nv = 96 ne = 84 npr = 22138 no. pairs analyzed = 22138 no. exposed pairs = 1530 no. arc points = 11131 no. surface atoms = 518 nbur = 640 mkacc time = 3.9999999E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 2293 m= 3 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1200000 number of dielectric boundary points 2402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 876 ## 76 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 4526 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0778808E-07 6.3934344E-08 midg,1,midg; midg,igrid,midg 1.0889569E-07 1.2724625E-07 1,midg,midg; igrid,midg,midg -1.0042752E-07 2.3854335E-07 gauss-seidel spectral radius is 0.9906139 estimated iterations to convergence 84 setup time was (sec) 0.3100000 now iterating at: 15:06:45 rms-change max change #iterations 0.1828691 27.27909 at 10iterations 2.4937309E-02 5.206938 at 20iterations 3.4253940E-03 0.6318283 at 30iterations 4.5994209E-04 7.1598053E-02 at 40iterations 6.2107290E-05 1.2893438E-02 at 50iterations finished qdiffx linear iterations at : 15:06:48 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 6.2107290E-05 1.2893438E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 15:06:49 3.493u 0.207s 0:04.26 86.6% 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 15 2011 at 15:06:49 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 # of charge parameter records: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1158 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.247097 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): -6.573000 32.12200 ymin,ymax (A): 0.8600000 39.64800 zmin,zma (A): -1.496000 46.03200 x,y,z range (A): 38.69500 38.78800 47.52800 scale (grids/A): 2.247097 object centre (A): 12.77450 20.25400 22.26800 number of atom coordinates read : 1158 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 85.99934 88.27573 85.19180 assigned negative charge : -169.8232 centred at (gu) : 85.11262 88.17641 85.35698 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 46571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11131 grid for indexing accessible points = 1.400000 m= 17416 mr = 30028 m= 3410 mr = 13052 m= 360 mr = 2352 m= 26 mr = 199 m= 0 mr = 17 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 22135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 44 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 8453 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) : 0.7490321 object centre at (A) : 12.77450 20.25400 22.26800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5695419E-02 6.9899540E-03 midg,1,midg; midg,igrid,midg 3.9341461E-02 3.2167017E-02 1,midg,midg; igrid,midg,midg -3.0713463E-02 4.2137764E-02 gauss-seidel spectral radius is 0.9988570 estimated iterations to convergence 234 setup time was (sec) 0.5200000 now iterating at: 15:06:50 rms-change max change #iterations 3.680115 202.4811 at 10iterations 1.830667 80.35505 at 20iterations 0.9118942 35.92382 at 30iterations 0.4557747 17.01705 at 40iterations 0.2263797 8.749267 at 50iterations 0.1131569 4.416275 at 60iterations 5.6356624E-02 2.463932 at 70iterations 2.8024012E-02 0.9954853 at 80iterations 1.3917988E-02 0.5029011 at 90iterations 6.9756145E-03 0.2738647 at 100iterations 3.4692141E-03 0.1326218 at 110iterations 1.7263878E-03 5.9127808E-02 at 120iterations finished qdiffx linear iterations at : 15:06:58 total time elapsed so far: 8.250000 # loops : 120 mean,max change (kT/e) : 1.7263878E-03 5.9127808E-02 energy calculations done at 8.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.390000 DelPhi exited at 15:06:58 8.391u 0.289s 0:09.05 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 Sat Oct 15 2011 at 15:06:58 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1158 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.370645 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): -6.573000 32.12200 ymin,ymax (A): 0.8600000 39.64800 zmin,zma (A): -1.496000 46.03200 x,y,z range (A): 38.69500 38.78800 47.52800 scale (grids/A): 3.370645 object centre (A): 12.77450 20.25400 22.26800 number of atom coordinates read : 1158 total number of charged atoms : 1061 net assigned charge : 5.500003 assigned positive charge : 175.3231 centred at (gu) : 83.99902 87.41367 82.78772 assigned negative charge : -169.8232 centred at (gu) : 82.66902 87.26469 83.03551 start vw surface at 5.0000001E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 107130 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11131 grid for indexing accessible points = 1.400000 m= 53650 mr = 72867 m= 22311 mr = 43645 m= 6502 mr = 18463 m= 1319 mr = 5142 m= 231 mr = 994 m= 28 mr = 175 m= 0 mr = 15 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7500000 number of dielectric boundary points 49870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 8488 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) : 2.247097 object centre at (A) : 12.77450 20.25400 22.26800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2811713 6.2312983E-02 midg,1,midg; midg,igrid,midg 0.3280250 0.2591648 1,midg,midg; igrid,midg,midg -0.2409699 0.2947299 gauss-seidel spectral radius is 0.9992980 estimated iterations to convergence 298 setup time was (sec) 1.000000 now iterating at: 15:06:59 rms-change max change #iterations 7.954340 294.1797 at 10iterations 4.636889 109.7471 at 20iterations 2.691967 64.89303 at 30iterations 1.567088 36.38274 at 40iterations 0.9098947 21.28992 at 50iterations 0.5286037 10.98003 at 60iterations 0.3059551 7.340940 at 70iterations 0.1779484 3.723997 at 80iterations 0.1031763 2.202304 at 90iterations 6.0127463E-02 1.307968 at 100iterations 3.4909066E-02 0.8407860 at 110iterations 2.0233950E-02 0.4209280 at 120iterations 1.1748369E-02 0.2624054 at 130iterations 6.8346844E-03 0.1415687 at 140iterations 3.9722645E-03 9.1621399E-02 at 150iterations 2.3115776E-03 4.7332048E-02 at 160iterations 1.3366155E-03 2.9007912E-02 at 170iterations 7.7845633E-04 1.5808105E-02 at 180iterations finished qdiffx linear iterations at : 15:07:11 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 7.7845633E-04 1.5808105E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 15:07:12 13.013u 0.271s 0:13.56 97.9% 0+0k 0+0io 0pf+0w