Mon Oct 10 16:07:27 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 Mon Oct 10 2011 at 16:07:27 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: GLM 350 has a net charge of -0.0940 !!! WARNING: GLM 505 has a net charge of -0.0940 !!! WARNING: ZN8 891 has a net charge of 1.4000 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: 0.5903031 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): -31.14600 17.62600 ymin,ymax (A): -8.389999 51.91800 zmin,zma (A): -17.90700 37.85800 x,y,z range (A): 48.77200 60.30800 55.76500 scale (grids/A): 0.5903031 object centre (A): -6.760000 21.76400 9.975499 number of atom coordinates read : 2756 total number of charged atoms : 2603 net assigned charge : 1.512015 assigned positive charge : 404.4606 centred at (gu) : 89.93104 87.45522 87.96497 assigned negative charge : -402.9497 centred at (gu) : 89.96880 87.43627 88.00993 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6466 nv = 96 ne = 84 npr = 55244 no. pairs analyzed = 55244 no. exposed pairs = 3721 no. arc points = 25752 no. surface atoms = 1251 nbur = 1505 mkacc time = 0.1600000 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 = 1.456000 m= 310 mr = 3342 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3416 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2473 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7980 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7105032E-09 -4.8957205E-10 midg,1,midg; midg,igrid,midg -1.6034149E-10 5.4712407E-10 1,midg,midg; igrid,midg,midg 1.5098772E-09 -5.8507588E-10 gauss-seidel spectral radius is 0.9851682 estimated iterations to convergence 67 setup time was (sec) 0.6300000 now iterating at: 16:07:27 rms-change max change #iterations 0.1038307 19.29026 at 10iterations 8.4890053E-03 1.477894 at 20iterations 8.6044474E-04 0.1365204 at 30iterations 2.1302552E-04 2.3651123E-02 at 40iterations 7.9666323E-05 8.7442398E-03 at 50iterations finished qdiffx linear iterations at : 16:07:31 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 7.9666323E-05 8.7442398E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 16:07:31 4.083u 0.256s 0:04.63 93.5% 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 Mon Oct 10 2011 at 16:07:31 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: GLM 350 has a net charge of -0.0940 !!! WARNING: GLM 505 has a net charge of -0.0940 !!! WARNING: ZN8 891 has a net charge of 1.4000 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: 1.770909 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): -31.14600 17.62600 ymin,ymax (A): -8.389999 51.91800 zmin,zma (A): -17.90700 37.85800 x,y,z range (A): 48.77200 60.30800 55.76500 scale (grids/A): 1.770909 object centre (A): -6.760000 21.76400 9.975499 number of atom coordinates read : 2756 total number of charged atoms : 2603 net assigned charge : 1.512015 assigned positive charge : 404.4606 centred at (gu) : 89.79232 82.36502 83.89450 assigned negative charge : -402.9497 centred at (gu) : 89.90626 82.30859 84.02953 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 70393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25752 grid for indexing accessible points = 1.400000 m= 23124 mr = 47549 m= 2972 mr = 15927 m= 130 mr = 1570 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 655 time to turn everything in is 0.6600000 number of dielectric boundary points 31550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 20244 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) : 0.5903031 object centre at (A) : -6.760000 21.76400 9.975499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1367880E-02 -2.0550988E-03 midg,1,midg; midg,igrid,midg 1.8235083E-03 -2.6836211E-02 1,midg,midg; igrid,midg,midg 4.8143207E-03 -3.0801474E-04 gauss-seidel spectral radius is 0.9984352 estimated iterations to convergence 201 setup time was (sec) 0.9500000 now iterating at: 16:07:32 rms-change max change #iterations 3.769460 155.8518 at 10iterations 1.663523 59.71832 at 20iterations 0.7414222 26.38254 at 30iterations 0.3285284 11.54952 at 40iterations 0.1447665 4.859866 at 50iterations 6.4482838E-02 2.084240 at 60iterations 2.8551012E-02 0.9312172 at 70iterations 1.2722702E-02 0.4295955 at 80iterations 5.7038255E-03 0.1957159 at 90iterations 2.5677148E-03 8.9522362E-02 at 100iterations 1.1864888E-03 4.0388107E-02 at 110iterations 5.7829119E-04 1.9312859E-02 at 120iterations finished qdiffx linear iterations at : 16:07:41 total time elapsed so far: 9.210000 # loops : 120 mean,max change (kT/e) : 5.7829119E-04 1.9312859E-02 energy calculations done at 9.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.380000 DelPhi exited at 16:07:41 9.387u 0.261s 0:09.93 97.0% 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 Mon Oct 10 2011 at 16:07:41 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: 276 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2756 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: GLM 350 has a net charge of -0.0940 !!! WARNING: GLM 505 has a net charge of -0.0940 !!! WARNING: ZN8 891 has a net charge of 1.4000 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: 2.656364 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): -31.14600 17.62600 ymin,ymax (A): -8.389999 51.91800 zmin,zma (A): -17.90700 37.85800 x,y,z range (A): 48.77200 60.30800 55.76500 scale (grids/A): 2.656364 object centre (A): -6.760000 21.76400 9.975499 number of atom coordinates read : 2756 total number of charged atoms : 2603 net assigned charge : 1.512015 assigned positive charge : 404.4606 centred at (gu) : 89.68836 78.54735 80.84145 assigned negative charge : -402.9497 centred at (gu) : 89.85920 78.46288 81.04427 start vw surface at 0.1700000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 163245 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25752 grid for indexing accessible points = 1.400000 m= 77055 mr = 116591 m= 24677 mr = 60325 m= 4902 mr = 18760 m= 516 mr = 3403 m= 20 mr = 295 m= 0 mr = 4 time to grow re-entrant surface = 0.9499999 no. cavity mid-points inaccessible to solvent = 2238 time to turn everything in is 1.590000 number of dielectric boundary points 71037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 20823 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) : 1.770909 object centre at (A) : -6.760000 21.76400 9.975499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1698211 -6.4123701E-04 midg,1,midg; midg,igrid,midg 0.1140149 -0.3955009 1,midg,midg; igrid,midg,midg 1.8768869E-02 -9.0233935E-03 gauss-seidel spectral radius is 0.9992154 estimated iterations to convergence 282 setup time was (sec) 1.910000 now iterating at: 16:07:43 rms-change max change #iterations 9.422376 336.9639 at 10iterations 5.519667 137.7128 at 20iterations 3.204585 81.97148 at 30iterations 1.850069 38.35888 at 40iterations 1.064340 22.59729 at 50iterations 0.6105511 12.64531 at 60iterations 0.3485973 6.892290 at 70iterations 0.1993025 4.641806 at 80iterations 0.1137499 2.471836 at 90iterations 6.4693987E-02 1.327689 at 100iterations 3.6916167E-02 0.7566156 at 110iterations 2.1011589E-02 0.4151201 at 120iterations 1.1908113E-02 0.2349796 at 130iterations 6.7908275E-03 0.1351471 at 140iterations 3.8667999E-03 7.9314947E-02 at 150iterations 2.2147037E-03 5.1596642E-02 at 160iterations 1.2795177E-03 2.6576519E-02 at 170iterations 7.5430289E-04 1.5450954E-02 at 180iterations finished qdiffx linear iterations at : 16:07:57 total time elapsed so far: 15.48000 # loops : 180 mean,max change (kT/e) : 7.5430289E-04 1.5450954E-02 energy calculations done at 15.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.66000 DelPhi exited at 16:07:58 15.664u 0.293s 0:16.22 98.3% 0+0k 0+0io 0pf+0w