Sun Oct 9 00:40:13 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 Sun Oct 9 2011 at 00:40:13 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2271 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6519191 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): -0.5390000 54.06900 ymin,ymax (A): -14.51700 27.56900 zmin,zma (A): 30.69700 83.97600 x,y,z range (A): 54.60800 42.08600 53.27900 scale (grids/A): 0.6519191 object centre (A): 26.76500 6.526000 57.33650 number of atom coordinates read : 2271 total number of charged atoms : 2137 net assigned charge : 11.50002 assigned positive charge : 330.4885 centred at (gu) : 90.39339 88.55070 88.91409 assigned negative charge : -318.9893 centred at (gu) : 90.41578 88.64301 88.90623 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6587 nv = 96 ne = 84 npr = 45595 no. pairs analyzed = 45595 no. exposed pairs = 2986 no. arc points = 21245 no. surface atoms = 994 nbur = 1277 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 375 mr = 3456 m= 3 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3469 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2085 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7770 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.7633723E-08 1.9447016E-08 midg,1,midg; midg,igrid,midg 4.7635819E-08 8.3224521E-09 1,midg,midg; igrid,midg,midg 2.4110316E-08 2.1905855E-08 gauss-seidel spectral radius is 0.9877833 estimated iterations to convergence 74 setup time was (sec) 0.4900000 now iterating at: 00:40:13 rms-change max change #iterations 0.1403878 22.29342 at 10iterations 1.4351287E-02 1.910820 at 20iterations 1.4868485E-03 0.2192459 at 30iterations 1.5982994E-04 2.4330139E-02 at 40iterations 1.8568568E-05 2.6512146E-03 at 50iterations finished qdiffx linear iterations at : 00:40:16 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 1.8568568E-05 2.6512146E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 00:40:16 3.063u 0.139s 0:03.51 90.8% 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 Sun Oct 9 2011 at 00:40:16 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2271 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: 1.955757 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): -0.5390000 54.06900 ymin,ymax (A): -14.51700 27.56900 zmin,zma (A): 30.69700 83.97600 x,y,z range (A): 54.60800 42.08600 53.27900 scale (grids/A): 1.955757 object centre (A): 26.76500 6.526000 57.33650 number of atom coordinates read : 2271 total number of charged atoms : 2137 net assigned charge : 11.50002 assigned positive charge : 330.4885 centred at (gu) : 91.18006 85.65177 86.74200 assigned negative charge : -318.9893 centred at (gu) : 91.24751 85.92898 86.71899 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70806 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21245 grid for indexing accessible points = 1.400000 m= 25369 mr = 47753 m= 4205 mr = 18278 m= 292 mr = 2483 m= 4 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 32074 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 16884 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) : 0.6519191 object centre at (A) : 26.76500 6.526000 57.33650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6414378E-02 4.8403949E-02 midg,1,midg; midg,igrid,midg 4.2468585E-02 -3.3879883E-03 1,midg,midg; igrid,midg,midg 5.7829972E-02 6.1429963E-02 gauss-seidel spectral radius is 0.9986755 estimated iterations to convergence 218 setup time was (sec) 0.7800000 now iterating at: 00:40:17 rms-change max change #iterations 3.973063 193.5810 at 10iterations 1.881462 71.89165 at 20iterations 0.8888789 28.09225 at 30iterations 0.4207394 17.35884 at 40iterations 0.1991215 6.150263 at 50iterations 9.4207279E-02 3.089615 at 60iterations 4.4515979E-02 1.517526 at 70iterations 2.1082455E-02 0.6667585 at 80iterations 9.9666016E-03 0.3832893 at 90iterations 4.7224266E-03 0.1486244 at 100iterations 2.2334927E-03 7.3570728E-02 at 110iterations 1.0583597E-03 3.6779404E-02 at 120iterations finished qdiffx linear iterations at : 00:40:23 total time elapsed so far: 6.700000 # loops : 120 mean,max change (kT/e) : 1.0583597E-03 3.6779404E-02 energy calculations done at 6.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.880000 DelPhi exited at 00:40:24 6.880u 0.148s 0:07.32 95.9% 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 Sun Oct 9 2011 at 00:40:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2271 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: 2.933636 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): -0.5390000 54.06900 ymin,ymax (A): -14.51700 27.56900 zmin,zma (A): 30.69700 83.97600 x,y,z range (A): 54.60800 42.08600 53.27900 scale (grids/A): 2.933636 object centre (A): 26.76500 6.526000 57.33650 number of atom coordinates read : 2271 total number of charged atoms : 2137 net assigned charge : 11.50002 assigned positive charge : 330.4885 centred at (gu) : 91.77000 83.47764 85.11298 assigned negative charge : -318.9893 centred at (gu) : 91.87125 83.89354 85.07842 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 163262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21245 grid for indexing accessible points = 1.400000 m= 81523 mr = 115951 m= 29943 mr = 65378 m= 7532 mr = 23635 m= 1155 mr = 5394 m= 63 mr = 731 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 72367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 17092 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) : 1.955757 object centre at (A) : 26.76500 6.526000 57.33650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2738226 0.6588351 midg,1,midg; midg,igrid,midg 0.4078388 -3.1597387E-02 1,midg,midg; igrid,midg,midg 0.6661911 0.6212571 gauss-seidel spectral radius is 0.9992734 estimated iterations to convergence 293 setup time was (sec) 1.510000 now iterating at: 00:40:25 rms-change max change #iterations 9.451287 404.6529 at 10iterations 5.574360 127.7341 at 20iterations 3.270084 75.27837 at 30iterations 1.910525 37.33511 at 40iterations 1.112560 24.75963 at 50iterations 0.6473600 13.15770 at 60iterations 0.3764737 6.942306 at 70iterations 0.2182271 4.530743 at 80iterations 0.1265237 2.478510 at 90iterations 7.3113710E-02 1.359087 at 100iterations 4.2328667E-02 0.7720795 at 110iterations 2.4517912E-02 0.4596004 at 120iterations 1.4195270E-02 0.2640551 at 130iterations 8.1999982E-03 0.1440220 at 140iterations 4.7404300E-03 9.6066952E-02 at 150iterations 2.7374362E-03 4.8664093E-02 at 160iterations 1.5876049E-03 2.8869629E-02 at 170iterations 9.1777556E-04 1.7453671E-02 at 180iterations finished qdiffx linear iterations at : 00:40:35 total time elapsed so far: 10.89000 # loops : 180 mean,max change (kT/e) : 9.1777556E-04 1.7453671E-02 energy calculations done at 10.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.07000 DelPhi exited at 00:40:35 11.075u 0.168s 0:11.50 97.6% 0+0k 0+0io 0pf+0w