Tue Oct 11 06:02:35 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 Tue Oct 11 2011 at 06:02:35 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7058030 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): 19.90600 63.99100 ymin,ymax (A): -3.445000 33.46700 zmin,zma (A): 21.58300 72.02200 x,y,z range (A): 44.08500 36.91200 50.43900 scale (grids/A): 0.7058030 object centre (A): 41.94850 15.01100 46.80250 number of atom coordinates read : 2061 total number of charged atoms : 1927 net assigned charge : 5.931010 assigned positive charge : 314.1441 centred at (gu) : 89.74278 89.79478 88.82440 assigned negative charge : -308.2131 centred at (gu) : 89.87070 89.83643 88.77666 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7151 nv = 96 ne = 84 npr = 40815 no. pairs analyzed = 40815 no. exposed pairs = 2467 no. arc points = 17004 no. surface atoms = 844 nbur = 1217 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 495 mr = 4214 m= 1 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1582 ## 139 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7737 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1645421E-08 5.6390483E-08 midg,1,midg; midg,igrid,midg 7.0441352E-08 2.7502958E-08 1,midg,midg; igrid,midg,midg 1.1315738E-07 -1.1959905E-08 gauss-seidel spectral radius is 0.9895356 estimated iterations to convergence 80 setup time was (sec) 0.5800000 now iterating at: 06:02:36 rms-change max change #iterations 0.2029234 30.43541 at 10iterations 2.5295809E-02 3.512446 at 20iterations 3.3262665E-03 0.4691658 at 30iterations 5.5587402E-04 7.7510834E-02 at 40iterations 1.3919440E-04 1.6607285E-02 at 50iterations finished qdiffx linear iterations at : 06:02:40 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 1.3919440E-04 1.6607285E-02 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 06:02:40 4.178u 0.248s 0:04.77 92.4% 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 06:02:40 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.117409 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): 19.90600 63.99100 ymin,ymax (A): -3.445000 33.46700 zmin,zma (A): 21.58300 72.02200 x,y,z range (A): 44.08500 36.91200 50.43900 scale (grids/A): 2.117409 object centre (A): 41.94850 15.01100 46.80250 number of atom coordinates read : 2061 total number of charged atoms : 1927 net assigned charge : 5.931010 assigned positive charge : 314.1441 centred at (gu) : 89.22836 89.38428 86.47327 assigned negative charge : -308.2131 centred at (gu) : 89.61227 89.50946 86.33024 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 75596 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17004 grid for indexing accessible points = 1.400000 m= 31323 mr = 54473 m= 6269 mr = 24096 m= 583 mr = 4263 m= 16 mr = 317 m= 0 mr = 3 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 30635 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15290 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) : 0.7058030 object centre at (A) : 41.94850 15.01100 46.80250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7821664E-02 4.8228607E-02 midg,1,midg; midg,igrid,midg 2.4871347E-02 9.8729059E-03 1,midg,midg; igrid,midg,midg 3.6881849E-02 1.9298645E-02 gauss-seidel spectral radius is 0.9988242 estimated iterations to convergence 231 setup time was (sec) 0.9100000 now iterating at: 06:02:41 rms-change max change #iterations 4.582823 169.1798 at 10iterations 2.268975 77.96300 at 20iterations 1.127176 33.25263 at 30iterations 0.5573001 17.08154 at 40iterations 0.2769414 8.472789 at 50iterations 0.1376006 3.972354 at 60iterations 6.8062678E-02 2.132013 at 70iterations 3.3800926E-02 0.9645321 at 80iterations 1.6843528E-02 0.5260687 at 90iterations 8.4763030E-03 0.2520447 at 100iterations 4.2402083E-03 0.1366816 at 110iterations 2.1692237E-03 6.6841602E-02 at 120iterations finished qdiffx linear iterations at : 06:02:50 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 2.1692237E-03 6.6841602E-02 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 06:02:51 9.395u 0.246s 0:10.70 90.0% 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 Tue Oct 11 2011 at 06:02:51 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.176114 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): 19.90600 63.99100 ymin,ymax (A): -3.445000 33.46700 zmin,zma (A): 21.58300 72.02200 x,y,z range (A): 44.08500 36.91200 50.43900 scale (grids/A): 3.176114 object centre (A): 41.94850 15.01100 46.80250 number of atom coordinates read : 2061 total number of charged atoms : 1927 net assigned charge : 5.931010 assigned positive charge : 314.1441 centred at (gu) : 88.84261 89.07669 84.70997 assigned negative charge : -308.2131 centred at (gu) : 89.41847 89.26423 84.49535 start vw surface at 0.1500000 fill in re-entrant regions at 0.8300000 boundary points on vw surface= 174148 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17004 grid for indexing accessible points = 1.400000 m= 96978 mr = 130734 m= 40569 mr = 81465 m= 11865 mr = 33721 m= 2384 mr = 9317 m= 283 mr = 1809 m= 17 mr = 190 m= 0 mr = 12 time to grow re-entrant surface = 0.9999999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.950000 number of dielectric boundary points 68996 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.110000 number of grid points assigned charge 15416 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) : 2.117409 object centre at (A) : 41.94850 15.01100 46.80250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1253077 0.3375126 midg,1,midg; midg,igrid,midg 0.1991985 6.4688444E-02 1,midg,midg; igrid,midg,midg 0.3362819 0.3263714 gauss-seidel spectral radius is 0.9992927 estimated iterations to convergence 297 setup time was (sec) 2.320000 now iterating at: 06:02:53 rms-change max change #iterations 10.26985 335.0336 at 10iterations 6.081854 127.2214 at 20iterations 3.588741 94.84550 at 30iterations 2.119301 41.31933 at 40iterations 1.246775 24.22122 at 50iterations 0.7309027 13.86015 at 60iterations 0.4290914 8.633924 at 70iterations 0.2514906 4.713913 at 80iterations 0.1474995 3.165467 at 90iterations 8.6417146E-02 2.187134 at 100iterations 5.0624419E-02 0.9493713 at 110iterations 2.9701883E-02 0.5132682 at 120iterations 1.7587932E-02 0.3040981 at 130iterations 1.0553031E-02 0.1991997 at 140iterations 6.4407499E-03 0.1152329 at 150iterations 4.0733763E-03 7.7579498E-02 at 160iterations 2.7016273E-03 4.4315338E-02 at 170iterations 1.9106998E-03 3.0250549E-02 at 180iterations finished qdiffx linear iterations at : 06:03:07 total time elapsed so far: 16.31000 # loops : 180 mean,max change (kT/e) : 1.9106998E-03 3.0250549E-02 energy calculations done at 16.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.48000 DelPhi exited at 06:03:08 16.485u 0.333s 0:17.33 96.9% 0+0k 0+0io 0pf+0w