Tue Oct 11 05:58:28 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 05:58:28 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2081 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7367855 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): -17.86100 30.45700 ymin,ymax (A): -11.64400 30.55600 zmin,zma (A): -8.456000 38.04400 x,y,z range (A): 48.31800 42.20000 46.50000 scale (grids/A): 0.7367855 object centre (A): 6.298000 9.455999 14.79400 number of atom coordinates read : 2081 total number of charged atoms : 1951 net assigned charge : 6.039010 assigned positive charge : 319.3160 centred at (gu) : 89.98413 89.72628 91.04248 assigned negative charge : -313.2771 centred at (gu) : 89.90430 89.64073 90.92394 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7721 nv = 96 ne = 84 npr = 42037 no. pairs analyzed = 42037 no. exposed pairs = 2503 no. arc points = 17035 no. surface atoms = 855 nbur = 1226 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 539 mr = 4560 m= 4 mr = 107 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.2900000 number of dielectric boundary points 3597 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1516 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8267 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.8681063E-09 2.5229281E-07 midg,1,midg; midg,igrid,midg 1.8649198E-08 1.6845561E-07 1,midg,midg; igrid,midg,midg 2.3473035E-08 1.7150124E-07 gauss-seidel spectral radius is 0.9903893 estimated iterations to convergence 83 setup time was (sec) 0.5200000 now iterating at: 05:58:29 rms-change max change #iterations 0.2406530 36.53313 at 10iterations 3.2998599E-02 4.693268 at 20iterations 4.6208920E-03 0.5357132 at 30iterations 7.3234952E-04 9.1270447E-02 at 40iterations 1.5229499E-04 1.7669678E-02 at 50iterations finished qdiffx linear iterations at : 05:58:31 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.5229499E-04 1.7669678E-02 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 05:58:32 3.493u 0.155s 0:04.10 88.7% 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 05:58:32 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2081 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.210356 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): -17.86100 30.45700 ymin,ymax (A): -11.64400 30.55600 zmin,zma (A): -8.456000 38.04400 x,y,z range (A): 48.31800 42.20000 46.50000 scale (grids/A): 2.210356 object centre (A): 6.298000 9.455999 14.79400 number of atom coordinates read : 2081 total number of charged atoms : 1951 net assigned charge : 6.039010 assigned positive charge : 319.3160 centred at (gu) : 89.95229 89.17909 93.12745 assigned negative charge : -313.2771 centred at (gu) : 89.71306 88.92210 92.77191 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81367 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17035 grid for indexing accessible points = 1.400000 m= 34237 mr = 58475 m= 7242 mr = 26502 m= 750 mr = 4985 m= 32 mr = 424 m= 0 mr = 3 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1255 time to turn everything in is 0.6400000 number of dielectric boundary points 33239 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 15526 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) : 0.7367855 object centre at (A) : 6.298000 9.455999 14.79400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9327455E-02 5.3612612E-02 midg,1,midg; midg,igrid,midg 2.7934425E-02 2.9232049E-02 1,midg,midg; igrid,midg,midg 3.9564785E-02 3.5994317E-02 gauss-seidel spectral radius is 0.9989082 estimated iterations to convergence 239 setup time was (sec) 0.9300000 now iterating at: 05:58:33 rms-change max change #iterations 4.985342 186.1147 at 10iterations 2.521430 83.17302 at 20iterations 1.287541 37.03220 at 30iterations 0.6536960 19.69007 at 40iterations 0.3302127 9.810026 at 50iterations 0.1688769 4.888692 at 60iterations 8.5695401E-02 2.366177 at 70iterations 4.3635447E-02 1.308544 at 80iterations 2.2295222E-02 0.6997375 at 90iterations 1.1429521E-02 0.3498497 at 100iterations 5.8813696E-03 0.1798077 at 110iterations 3.0325598E-03 8.3200455E-02 at 120iterations finished qdiffx linear iterations at : 05:58:40 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 3.0325598E-03 8.3200455E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 05:58:41 7.952u 0.207s 0:08.57 95.0% 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 05:58:41 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2081 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 3.315535 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): -17.86100 30.45700 ymin,ymax (A): -11.64400 30.55600 zmin,zma (A): -8.456000 38.04400 x,y,z range (A): 48.31800 42.20000 46.50000 scale (grids/A): 3.315535 object centre (A): 6.298000 9.455999 14.79400 number of atom coordinates read : 2081 total number of charged atoms : 1951 net assigned charge : 6.039010 assigned positive charge : 319.3160 centred at (gu) : 89.92847 88.76878 94.69119 assigned negative charge : -313.2771 centred at (gu) : 89.56959 88.38322 94.15793 start vw surface at 0.2200000 fill in re-entrant regions at 1.000000 boundary points on vw surface= 186983 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17035 grid for indexing accessible points = 1.400000 m= 104821 mr = 139894 m= 45076 mr = 88267 m= 14076 mr = 37681 m= 3073 mr = 11182 m= 431 mr = 2327 m= 18 mr = 258 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 4183 time to turn everything in is 2.150000 number of dielectric boundary points 74869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 15608 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) : 2.210356 object centre at (A) : 6.298000 9.455999 14.79400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5463327 0.4619547 midg,1,midg; midg,igrid,midg 0.2405318 0.1497434 1,midg,midg; igrid,midg,midg 0.2071306 0.1625569 gauss-seidel spectral radius is 0.9993154 estimated iterations to convergence 302 setup time was (sec) 2.460000 now iterating at: 05:58:43 rms-change max change #iterations 10.89149 326.7515 at 10iterations 6.477735 127.3548 at 20iterations 3.841526 85.52064 at 30iterations 2.282368 41.84176 at 40iterations 1.351970 25.41239 at 50iterations 0.7986317 13.06216 at 60iterations 0.4720455 7.948811 at 70iterations 0.2786162 4.465449 at 80iterations 0.1643248 2.613366 at 90iterations 9.7214572E-02 1.566450 at 100iterations 5.7464477E-02 1.044109 at 110iterations 3.4190539E-02 0.5540009 at 120iterations 2.0462833E-02 0.3579636 at 130iterations 1.2445102E-02 0.2242203 at 140iterations 7.7689853E-03 0.1392746 at 150iterations 5.0339187E-03 9.1949463E-02 at 160iterations 3.4246393E-03 6.2049866E-02 at 170iterations 2.4688379E-03 4.4448853E-02 at 180iterations finished qdiffx linear iterations at : 05:58:54 total time elapsed so far: 12.77000 # loops : 180 mean,max change (kT/e) : 2.4688379E-03 4.4448853E-02 energy calculations done at 12.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.96000 DelPhi exited at 05:58:54 12.961u 0.183s 0:13.44 97.7% 0+0k 0+0io 0pf+0w