Tue Oct 11 04:31:02 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 04:31:02 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2767 !!! WARNING: ASP 28 has a net charge of -2.0000 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6359868 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): -11.13200 37.16100 ymin,ymax (A): -25.91000 22.68700 zmin,zma (A): -10.70200 45.27400 x,y,z range (A): 48.29300 48.59700 55.97600 scale (grids/A): 0.6359868 object centre (A): 13.01450 -1.611500 17.28600 number of atom coordinates read : 2767 total number of charged atoms : 2614 net assigned charge : -1.859980 assigned positive charge : 417.2437 centred at (gu) : 89.81459 90.44275 92.11121 assigned negative charge : -419.1043 centred at (gu) : 89.54283 90.35231 92.07327 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7352 nv = 96 ne = 84 npr = 57080 no. pairs analyzed = 57080 no. exposed pairs = 3385 no. arc points = 23370 no. surface atoms = 1146 nbur = 1621 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 375 mr = 4098 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2367 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8994 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2856505E-09 2.9851299E-09 midg,1,midg; midg,igrid,midg -1.1530614E-08 8.4128189E-09 1,midg,midg; igrid,midg,midg -3.5285879E-08 2.6101924E-08 gauss-seidel spectral radius is 0.9872023 estimated iterations to convergence 72 setup time was (sec) 0.4000000 now iterating at: 04:31:02 rms-change max change #iterations 0.1480522 22.31355 at 10iterations 1.4535067E-02 2.066752 at 20iterations 1.4919079E-03 0.2287273 at 30iterations 1.7445280E-04 2.7343750E-02 at 40iterations 3.1958170E-05 5.1984787E-03 at 50iterations finished qdiffx linear iterations at : 04:31:05 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 3.1958170E-05 5.1984787E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 04:31:06 3.416u 0.174s 0:04.15 86.2% 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 04:31:06 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2767 !!! WARNING: ASP 28 has a net charge of -2.0000 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.907961 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): -11.13200 37.16100 ymin,ymax (A): -25.91000 22.68700 zmin,zma (A): -10.70200 45.27400 x,y,z range (A): 48.29300 48.59700 55.97600 scale (grids/A): 1.907961 object centre (A): 13.01450 -1.611500 17.28600 number of atom coordinates read : 2767 total number of charged atoms : 2614 net assigned charge : -1.859980 assigned positive charge : 417.2437 centred at (gu) : 89.44324 91.32761 96.33305 assigned negative charge : -419.1043 centred at (gu) : 88.62837 91.05674 96.21961 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23370 grid for indexing accessible points = 1.400000 m= 28852 mr = 55779 m= 4467 mr = 21370 m= 226 mr = 2713 m= 5 mr = 74 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 225 time to turn everything in is 0.3800000 number of dielectric boundary points 33110 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 192 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 20566 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) : 0.6359868 object centre at (A) : 13.01450 -1.611500 17.28600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3860206E-02 -1.8460672E-02 midg,1,midg; midg,igrid,midg -1.0857956E-02 1.4406869E-02 1,midg,midg; igrid,midg,midg -2.0804271E-02 4.8452619E-02 gauss-seidel spectral radius is 0.9986541 estimated iterations to convergence 216 setup time was (sec) 0.6100000 now iterating at: 04:31:07 rms-change max change #iterations 4.407750 191.8266 at 10iterations 2.077775 74.36105 at 20iterations 0.9827967 30.47553 at 30iterations 0.4634943 15.74343 at 40iterations 0.2189305 7.164646 at 50iterations 0.1035060 3.147550 at 60iterations 4.8816800E-02 1.557365 at 70iterations 2.3043931E-02 0.7160745 at 80iterations 1.0862517E-02 0.3225322 at 90iterations 5.1232874E-03 0.1515905 at 100iterations 2.4250182E-03 7.7132106E-02 at 110iterations 1.1452280E-03 3.6533356E-02 at 120iterations finished qdiffx linear iterations at : 04:31:14 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.1452280E-03 3.6533356E-02 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 04:31:14 7.786u 0.212s 0:08.28 96.4% 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 04:31:14 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2767 !!! WARNING: ASP 28 has a net charge of -2.0000 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.861941 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): -11.13200 37.16100 ymin,ymax (A): -25.91000 22.68700 zmin,zma (A): -10.70200 45.27400 x,y,z range (A): 48.29300 48.59700 55.97600 scale (grids/A): 2.861941 object centre (A): 13.01450 -1.611500 17.28600 number of atom coordinates read : 2767 total number of charged atoms : 2614 net assigned charge : -1.859980 assigned positive charge : 417.2437 centred at (gu) : 89.16480 91.99134 99.49968 assigned negative charge : -419.1043 centred at (gu) : 87.94240 91.58511 99.32927 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 183858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23370 grid for indexing accessible points = 1.400000 m= 94171 mr = 135139 m= 33627 mr = 77227 m= 7848 mr = 26909 m= 1040 mr = 5883 m= 50 mr = 654 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 825 time to turn everything in is 1.000000 number of dielectric boundary points 74761 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 20906 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) : 1.907961 object centre at (A) : 13.01450 -1.611500 17.28600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.9191946 0.1724146 midg,1,midg; midg,igrid,midg -0.1395571 0.2075259 1,midg,midg; igrid,midg,midg -0.1231681 0.4563713 gauss-seidel spectral radius is 0.9992633 estimated iterations to convergence 291 setup time was (sec) 1.250000 now iterating at: 04:31:16 rms-change max change #iterations 10.36138 375.3478 at 10iterations 6.053717 124.8541 at 20iterations 3.521868 86.07482 at 30iterations 2.049582 47.83647 at 40iterations 1.185468 22.53981 at 50iterations 0.6858584 13.25985 at 60iterations 0.3969959 6.831378 at 70iterations 0.2295994 4.452034 at 80iterations 0.1325332 2.394906 at 90iterations 7.6421782E-02 1.604470 at 100iterations 4.4199776E-02 0.7828894 at 110iterations 2.5461424E-02 0.4645844 at 120iterations 1.4698191E-02 0.2846756 at 130iterations 8.4826760E-03 0.1498623 at 140iterations 4.9020308E-03 8.1459045E-02 at 150iterations 2.8406968E-03 4.8051834E-02 at 160iterations 1.6503669E-03 2.9644489E-02 at 170iterations 9.6190575E-04 1.8039703E-02 at 180iterations finished qdiffx linear iterations at : 04:31:27 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 9.6190575E-04 1.8039703E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 04:31:28 12.634u 0.201s 0:13.18 97.3% 0+0k 0+0io 0pf+0w