Mon Oct 10 00:11:37 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 00:11:37 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3111 !!! WARNING: SEP 140 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6331252 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): -34.79300 19.37200 ymin,ymax (A): -13.47500 37.70400 zmin,zma (A): -14.41500 41.81400 x,y,z range (A): 54.16500 51.17900 56.22900 scale (grids/A): 0.6331252 object centre (A): -7.710502 12.11450 13.69950 number of atom coordinates read : 3111 total number of charged atoms : 2967 net assigned charge : 2.025009 assigned positive charge : 470.9520 centred at (gu) : 91.02043 90.42227 91.43219 assigned negative charge : -468.9282 centred at (gu) : 90.99944 90.33096 91.39288 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8359 nv = 96 ne = 84 npr = 61899 no. pairs analyzed = 61899 no. exposed pairs = 4054 no. arc points = 28958 no. surface atoms = 1348 nbur = 1763 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 4439 m= 4 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3400000 number of dielectric boundary points 4335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2853 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 10173 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6742838E-09 9.3090069E-09 midg,1,midg; midg,igrid,midg -7.7032647E-09 1.4007314E-08 1,midg,midg; igrid,midg,midg -1.2636911E-10 5.8523586E-09 gauss-seidel spectral radius is 0.9871284 estimated iterations to convergence 72 setup time was (sec) 0.6100000 now iterating at: 00:11:38 rms-change max change #iterations 0.1513409 19.71266 at 10iterations 1.4648647E-02 1.959976 at 20iterations 1.4315685E-03 0.2014923 at 30iterations 1.4012076E-04 1.8150330E-02 at 40iterations 1.4225360E-05 1.7566681E-03 at 50iterations finished qdiffx linear iterations at : 00:11:42 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 1.4225360E-05 1.7566681E-03 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 00:11:42 4.230u 0.233s 0:04.74 94.0% 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 00:11:42 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3111 !!! WARNING: SEP 140 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.899376 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): -34.79300 19.37200 ymin,ymax (A): -13.47500 37.70400 zmin,zma (A): -14.41500 41.81400 x,y,z range (A): 54.16500 51.17900 56.22900 scale (grids/A): 1.899376 object centre (A): -7.710502 12.11450 13.69950 number of atom coordinates read : 3111 total number of charged atoms : 2967 net assigned charge : 2.025009 assigned positive charge : 470.9520 centred at (gu) : 93.06070 91.26586 94.29608 assigned negative charge : -468.9282 centred at (gu) : 92.99796 90.99280 94.17847 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 90545 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28958 grid for indexing accessible points = 1.400000 m= 30765 mr = 61460 m= 4413 mr = 21870 m= 215 mr = 2572 m= 0 mr = 73 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 3109 time to turn everything in is 0.6600000 number of dielectric boundary points 39963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 190 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 23334 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) : 0.6331252 object centre at (A) : -7.710502 12.11450 13.69950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6521406E-03 5.6038555E-03 midg,1,midg; midg,igrid,midg -2.7976870E-03 1.1359646E-02 1,midg,midg; igrid,midg,midg -1.8205561E-02 5.5349553E-03 gauss-seidel spectral radius is 0.9986892 estimated iterations to convergence 219 setup time was (sec) 0.9900000 now iterating at: 00:11:43 rms-change max change #iterations 4.681525 204.8219 at 10iterations 2.219176 75.53902 at 20iterations 1.050231 31.44669 at 30iterations 0.4993885 15.80754 at 40iterations 0.2374213 7.039232 at 50iterations 0.1125129 3.268901 at 60iterations 5.3655274E-02 1.567022 at 70iterations 2.5372867E-02 0.6997986 at 80iterations 1.2098599E-02 0.3650799 at 90iterations 5.7389797E-03 0.1728859 at 100iterations 2.7189127E-03 8.2406044E-02 at 110iterations 1.2925579E-03 3.6983490E-02 at 120iterations finished qdiffx linear iterations at : 00:11:52 total time elapsed so far: 9.670000 # loops : 120 mean,max change (kT/e) : 1.2925579E-03 3.6983490E-02 energy calculations done at 9.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.870000 DelPhi exited at 00:11:53 9.868u 0.268s 0:10.42 97.1% 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 Mon Oct 10 2011 at 00:11:53 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3111 !!! WARNING: SEP 140 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.849064 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): -34.79300 19.37200 ymin,ymax (A): -13.47500 37.70400 zmin,zma (A): -14.41500 41.81400 x,y,z range (A): 54.16500 51.17900 56.22900 scale (grids/A): 2.849064 object centre (A): -7.710502 12.11450 13.69950 number of atom coordinates read : 3111 total number of charged atoms : 2967 net assigned charge : 2.025009 assigned positive charge : 470.9520 centred at (gu) : 94.59077 91.89861 96.44397 assigned negative charge : -468.9282 centred at (gu) : 94.49663 91.48908 96.26738 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 209705 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28958 grid for indexing accessible points = 1.400000 m= 101302 mr = 149461 m= 34379 mr = 81525 m= 7648 mr = 26797 m= 952 mr = 5538 m= 29 mr = 608 m= 0 mr = 14 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 10562 time to turn everything in is 1.700000 number of dielectric boundary points 90072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.860000 number of grid points assigned charge 23734 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) : 1.899376 object centre at (A) : -7.710502 12.11450 13.69950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1578044 2.6571549E-02 midg,1,midg; midg,igrid,midg 4.6991199E-02 -0.1406057 1,midg,midg; igrid,midg,midg -0.3099063 -4.6084300E-02 gauss-seidel spectral radius is 0.9992985 estimated iterations to convergence 298 setup time was (sec) 2.050000 now iterating at: 00:11:55 rms-change max change #iterations 11.18633 392.0432 at 10iterations 6.732108 158.3222 at 20iterations 4.019403 114.1093 at 30iterations 2.382144 45.54232 at 40iterations 1.406299 25.02235 at 50iterations 0.8290621 13.88941 at 60iterations 0.4872319 8.394589 at 70iterations 0.2855363 5.073453 at 80iterations 0.1675741 4.017502 at 90iterations 9.8212488E-02 1.554926 at 100iterations 5.7268806E-02 1.049299 at 110iterations 3.3551406E-02 0.5813804 at 120iterations 1.9571094E-02 0.3269665 at 130iterations 1.1423770E-02 0.1831322 at 140iterations 6.6842865E-03 0.1233044 at 150iterations 3.8951722E-03 8.3472252E-02 at 160iterations 2.2746581E-03 3.7037849E-02 at 170iterations 1.3280432E-03 2.2235870E-02 at 180iterations finished qdiffx linear iterations at : 00:12:09 total time elapsed so far: 15.92000 # loops : 180 mean,max change (kT/e) : 1.3280432E-03 2.2235870E-02 energy calculations done at 15.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.11000 DelPhi exited at 00:12:09 16.109u 0.295s 0:16.69 98.2% 0+0k 0+0io 0pf+0w