Sun Oct 9 20:54:33 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 Sun Oct 9 2011 at 20:54:33 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3147 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6673665 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): 45.30900 98.19300 ymin,ymax (A): 2.810000 56.15400 zmin,zma (A): 15.28200 67.79000 x,y,z range (A): 52.88400 53.34400 52.50800 scale (grids/A): 0.6673665 object centre (A): 71.75100 29.48200 41.53600 number of atom coordinates read : 3147 total number of charged atoms : 2998 net assigned charge : 9.225015 assigned positive charge : 479.2408 centred at (gu) : 90.50694 88.60316 90.52347 assigned negative charge : -470.0171 centred at (gu) : 90.41079 88.48895 90.51910 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 9598 nv = 96 ne = 84 npr = 62238 no. pairs analyzed = 62238 no. exposed pairs = 3955 no. arc points = 28537 no. surface atoms = 1318 nbur = 1829 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 571 mr = 5245 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 55 time to turn everything in is 0.2400000 number of dielectric boundary points 4845 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2768 ## 252 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 11229 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4908966E-08 3.3457692E-08 midg,1,midg; midg,igrid,midg -6.5975905E-09 4.6232447E-08 1,midg,midg; igrid,midg,midg 9.6330122E-10 6.2462227E-08 gauss-seidel spectral radius is 0.9884194 estimated iterations to convergence 76 setup time was (sec) 0.4300000 now iterating at: 20:54:34 rms-change max change #iterations 0.1979476 29.46213 at 10iterations 2.1575790E-02 2.715994 at 20iterations 2.3386176E-03 0.2869625 at 30iterations 2.6045655E-04 3.1929016E-02 at 40iterations 2.8223441E-05 3.4277439E-03 at 50iterations finished qdiffx linear iterations at : 20:54:37 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 2.8223441E-05 3.4277439E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 20:54:37 3.449u 0.169s 0:03.95 91.1% 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 Sun Oct 9 2011 at 20:54:37 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3147 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.002100 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): 45.30900 98.19300 ymin,ymax (A): 2.810000 56.15400 zmin,zma (A): 15.28200 67.79000 x,y,z range (A): 52.88400 53.34400 52.50800 scale (grids/A): 2.002100 object centre (A): 71.75100 29.48200 41.53600 number of atom coordinates read : 3147 total number of charged atoms : 2998 net assigned charge : 9.225015 assigned positive charge : 479.2408 centred at (gu) : 91.52020 85.80863 91.56955 assigned negative charge : -470.0171 centred at (gu) : 91.23187 85.46658 91.55711 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 102802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28537 grid for indexing accessible points = 1.400000 m= 37671 mr = 71252 m= 6751 mr = 27642 m= 572 mr = 4287 m= 21 mr = 291 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 2157 time to turn everything in is 0.5000000 number of dielectric boundary points 44345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 141 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 23749 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) : 0.6673665 object centre at (A) : 71.75100 29.48200 41.53600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3658090E-03 -1.5503453E-02 midg,1,midg; midg,igrid,midg 9.7063161E-02 7.3328406E-02 1,midg,midg; igrid,midg,midg 1.2734477E-02 3.5754751E-02 gauss-seidel spectral radius is 0.9988179 estimated iterations to convergence 230 setup time was (sec) 0.7200000 now iterating at: 20:54:38 rms-change max change #iterations 5.241068 180.9544 at 10iterations 2.591193 89.31177 at 20iterations 1.271879 34.75998 at 30iterations 0.6276044 18.61331 at 40iterations 0.3089713 9.168200 at 50iterations 0.1523065 4.250642 at 60iterations 7.5362951E-02 2.211109 at 70iterations 3.7092298E-02 0.9933033 at 80iterations 1.8325374E-02 0.4931717 at 90iterations 9.0477187E-03 0.2416725 at 100iterations 4.4577881E-03 0.1150973 at 110iterations 2.2029672E-03 5.9329987E-02 at 120iterations finished qdiffx linear iterations at : 20:54:45 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 2.2029672E-03 5.9329987E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 20:54:46 8.100u 0.192s 0:08.60 96.3% 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 20:54:46 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3147 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: SEP 139 has a net charge of -0.4750 !!! WARNING: CYS 258 has a net charge of 0.5000 !!! WARNING: GLM 422 has a net charge of -0.6000 !!! WARNING: GLM 556 has a net charge of -0.6000 !!! WARNING: ZN7 776 has a net charge of 1.4000 !!! WARNING: ZN7 780 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.003149 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): 45.30900 98.19300 ymin,ymax (A): 2.810000 56.15400 zmin,zma (A): 15.28200 67.79000 x,y,z range (A): 52.88400 53.34400 52.50800 scale (grids/A): 3.003149 object centre (A): 71.75100 29.48200 41.53600 number of atom coordinates read : 3147 total number of charged atoms : 2998 net assigned charge : 9.225015 assigned positive charge : 479.2408 centred at (gu) : 92.27998 83.71271 92.35414 assigned negative charge : -470.0171 centred at (gu) : 91.84756 83.19984 92.33545 start vw surface at 0.1100000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 237716 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28537 grid for indexing accessible points = 1.400000 m= 120520 mr = 172461 m= 45198 mr = 98415 m= 12347 mr = 36146 m= 2310 mr = 9434 m= 270 mr = 1635 m= 5 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.7600000 no. cavity mid-points inaccessible to solvent = 7373 time to turn everything in is 1.320000 number of dielectric boundary points 100097 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 23984 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) : 2.002100 object centre at (A) : 71.75100 29.48200 41.53600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1454672 -0.3497140 midg,1,midg; midg,igrid,midg 0.6418975 0.5058413 1,midg,midg; igrid,midg,midg 0.2605352 0.4848227 gauss-seidel spectral radius is 0.9993260 estimated iterations to convergence 304 setup time was (sec) 1.580000 now iterating at: 20:54:48 rms-change max change #iterations 12.09361 474.7242 at 10iterations 7.275523 188.5771 at 20iterations 4.354847 89.35678 at 30iterations 2.612615 50.15465 at 40iterations 1.553911 30.52551 at 50iterations 0.9237253 20.42757 at 60iterations 0.5489826 11.35244 at 70iterations 0.3259296 5.110070 at 80iterations 0.1929204 3.387764 at 90iterations 0.1141913 1.876170 at 100iterations 6.7579143E-02 1.237368 at 110iterations 3.9954394E-02 0.6084957 at 120iterations 2.3611480E-02 0.3722627 at 130iterations 1.3965428E-02 0.2410164 at 140iterations 8.2417093E-03 0.1310463 at 150iterations 4.8605492E-03 7.4783325E-02 at 160iterations 2.8741765E-03 4.3159485E-02 at 170iterations 1.6988610E-03 2.7629852E-02 at 180iterations finished qdiffx linear iterations at : 20:55:00 total time elapsed so far: 13.50000 # loops : 180 mean,max change (kT/e) : 1.6988610E-03 2.7629852E-02 energy calculations done at 13.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.64000 DelPhi exited at 20:55:00 13.643u 0.209s 0:14.12 98.0% 0+0k 0+0io 0pf+0w