Tue Oct 11 03:18:12 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 03:18:12 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3416 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: SER 496 has a net charge of -0.2720 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: 0.5785514 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): -11.31100 43.93900 ymin,ymax (A): 14.40600 75.11300 zmin,zma (A): 39.97500 101.5080 x,y,z range (A): 55.25000 60.70700 61.53300 scale (grids/A): 0.5785514 object centre (A): 16.31400 44.75950 70.74150 number of atom coordinates read : 3416 total number of charged atoms : 3271 net assigned charge : -7.612968 assigned positive charge : 517.7385 centred at (gu) : 88.35552 87.78332 88.43868 assigned negative charge : -525.3528 centred at (gu) : 88.38828 87.78622 88.44739 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7390 nv = 96 ne = 84 npr = 70056 no. pairs analyzed = 70056 no. exposed pairs = 4422 no. arc points = 30715 no. surface atoms = 1482 nbur = 1934 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 361 mr = 3820 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3164 ## 348 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 9510 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9544508E-09 -1.2613248E-09 midg,1,midg; midg,igrid,midg -2.5159967E-09 -1.0049052E-09 1,midg,midg; igrid,midg,midg -1.1205994E-09 -1.6391127E-09 gauss-seidel spectral radius is 0.9846140 estimated iterations to convergence 66 setup time was (sec) 0.4300000 now iterating at: 03:18:13 rms-change max change #iterations 0.1081193 16.61143 at 10iterations 8.6184023E-03 1.304300 at 20iterations 7.3427544E-04 9.8586082E-02 at 30iterations 1.1400104E-04 1.4886856E-02 at 40iterations 3.1603035E-05 5.0668716E-03 at 50iterations finished qdiffx linear iterations at : 03:18:16 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 3.1603035E-05 5.0668716E-03 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 03:18:16 3.422u 0.173s 0:03.90 92.0% 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 03:18:16 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3416 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: SER 496 has a net charge of -0.2720 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: 1.735654 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): -11.31100 43.93900 ymin,ymax (A): 14.40600 75.11300 zmin,zma (A): 39.97500 101.5080 x,y,z range (A): 55.25000 60.70700 61.53300 scale (grids/A): 1.735654 object centre (A): 16.31400 44.75950 70.74150 number of atom coordinates read : 3416 total number of charged atoms : 3271 net assigned charge : -7.612968 assigned positive charge : 517.7385 centred at (gu) : 85.06542 83.34895 85.31526 assigned negative charge : -525.3528 centred at (gu) : 85.16422 83.35800 85.34181 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79624 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30715 grid for indexing accessible points = 1.400000 m= 28149 mr = 53233 m= 3764 mr = 20144 m= 141 mr = 1962 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 36324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 239 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 25317 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) : 0.5785514 object centre at (A) : 16.31400 44.75950 70.74150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7852260E-02 1.9008132E-02 midg,1,midg; midg,igrid,midg -3.0706576E-03 2.8389252E-03 1,midg,midg; igrid,midg,midg -3.7201971E-03 4.7782465E-04 gauss-seidel spectral radius is 0.9984363 estimated iterations to convergence 201 setup time was (sec) 0.6100000 now iterating at: 03:18:17 rms-change max change #iterations 4.141591 168.4344 at 10iterations 1.830533 58.61495 at 20iterations 0.8130900 30.35946 at 30iterations 0.3595175 12.09278 at 40iterations 0.1596803 5.409431 at 50iterations 7.0881605E-02 2.280839 at 60iterations 3.1460691E-02 0.9481773 at 70iterations 1.4010343E-02 0.4602337 at 80iterations 6.2200380E-03 0.2100105 at 90iterations 2.8017426E-03 9.1745377E-02 at 100iterations 1.2635607E-03 4.3029785E-02 at 110iterations 5.8465975E-04 1.8041611E-02 at 120iterations finished qdiffx linear iterations at : 03:18:24 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 5.8465975E-04 1.8041611E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 03:18:25 7.841u 0.209s 0:08.50 94.5% 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 03:18:25 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: 331 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3416 !!! WARNING: GLM 16 has a net charge of -0.0940 !!! WARNING: GLU 164 has a net charge of -0.2720 !!! WARNING: SEP 224 has a net charge of -0.4750 !!! WARNING: SER 496 has a net charge of -0.2720 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: 2.603481 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): -11.31100 43.93900 ymin,ymax (A): 14.40600 75.11300 zmin,zma (A): 39.97500 101.5080 x,y,z range (A): 55.25000 60.70700 61.53300 scale (grids/A): 2.603481 object centre (A): 16.31400 44.75950 70.74150 number of atom coordinates read : 3416 total number of charged atoms : 3271 net assigned charge : -7.612968 assigned positive charge : 517.7385 centred at (gu) : 82.59805 80.02322 82.97261 assigned negative charge : -525.3528 centred at (gu) : 82.74622 80.03690 83.01266 start vw surface at 0.1000000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 184113 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30715 grid for indexing accessible points = 1.400000 m= 91712 mr = 130078 m= 31885 mr = 73357 m= 6351 mr = 24784 m= 610 mr = 4182 m= 26 mr = 263 m= 0 mr = 3 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.020000 number of dielectric boundary points 82030 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 26152 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) : 1.735654 object centre at (A) : 16.31400 44.75950 70.74150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4003154 0.3798923 midg,1,midg; midg,igrid,midg 5.3253986E-02 0.2974461 1,midg,midg; igrid,midg,midg -6.7979204E-03 -2.2305990E-02 gauss-seidel spectral radius is 0.9992267 estimated iterations to convergence 284 setup time was (sec) 1.250000 now iterating at: 03:18:26 rms-change max change #iterations 10.41590 304.0531 at 10iterations 6.101072 133.0574 at 20iterations 3.522925 72.47206 at 30iterations 2.033324 44.93346 at 40iterations 1.168094 25.33160 at 50iterations 0.6699071 14.91557 at 60iterations 0.3829008 7.949921 at 70iterations 0.2184734 4.478904 at 80iterations 0.1245800 2.661294 at 90iterations 7.1112335E-02 1.432145 at 100iterations 4.0400945E-02 0.7411919 at 110iterations 2.2997741E-02 0.4218197 at 120iterations 1.3076426E-02 0.2329466 at 130iterations 7.4179019E-03 0.1462556 at 140iterations 4.2185057E-03 7.4445248E-02 at 150iterations 2.3989738E-03 4.7134399E-02 at 160iterations 1.3627933E-03 2.7107239E-02 at 170iterations 7.7737740E-04 1.4886856E-02 at 180iterations finished qdiffx linear iterations at : 03:18:38 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 7.7737740E-04 1.4886856E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 03:18:38 12.824u 0.218s 0:13.32 97.8% 0+0k 0+0io 0pf+0w