Tue Oct 11 03:35:29 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 03:35:29 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2186 !!! WARNING: ASL 331 has a net charge of -0.1000 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: GLU 460 has a net charge of -2.0000 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: 0.6115683 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): -15.56700 26.99000 ymin,ymax (A): -2.479000 51.40600 zmin,zma (A): -5.068000 53.14300 x,y,z range (A): 42.55700 53.88500 58.21100 scale (grids/A): 0.6115683 object centre (A): 5.711500 24.46350 24.03750 number of atom coordinates read : 2186 total number of charged atoms : 2088 net assigned charge : -6.585979 assigned positive charge : 323.1335 centred at (gu) : 89.16443 89.42011 89.13503 assigned negative charge : -329.7199 centred at (gu) : 89.01128 89.52954 89.15979 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5525 nv = 96 ne = 84 npr = 44636 no. pairs analyzed = 44636 no. exposed pairs = 2761 no. arc points = 19782 no. surface atoms = 938 nbur = 1248 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 267 mr = 2951 m= 0 mr = 19 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1879 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6712 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5580183E-09 -4.2607669E-09 midg,1,midg; midg,igrid,midg 8.3907076E-10 -7.8480360E-09 1,midg,midg; igrid,midg,midg -1.3151247E-08 2.0987552E-09 gauss-seidel spectral radius is 0.9861267 estimated iterations to convergence 70 setup time was (sec) 0.4800000 now iterating at: 03:35:30 rms-change max change #iterations 0.1105264 19.27492 at 10iterations 9.7065773E-03 1.660104 at 20iterations 8.7203563E-04 0.1460991 at 30iterations 7.5591262E-05 1.1360168E-02 at 40iterations 6.7696760E-06 1.0213852E-03 at 50iterations finished qdiffx linear iterations at : 03:35:32 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 6.7696760E-06 1.0213852E-03 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 03:35:33 3.192u 0.164s 0:03.68 91.0% 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 03:35:33 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2186 !!! WARNING: ASL 331 has a net charge of -0.1000 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: GLU 460 has a net charge of -2.0000 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: 1.834705 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): -15.56700 26.99000 ymin,ymax (A): -2.479000 51.40600 zmin,zma (A): -5.068000 53.14300 x,y,z range (A): 42.55700 53.88500 58.21100 scale (grids/A): 1.834705 object centre (A): 5.711500 24.46350 24.03750 number of atom coordinates read : 2186 total number of charged atoms : 2088 net assigned charge : -6.585979 assigned positive charge : 323.1335 centred at (gu) : 87.49290 88.26008 87.40501 assigned negative charge : -329.7199 centred at (gu) : 87.03384 88.58849 87.47927 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19782 grid for indexing accessible points = 1.400000 m= 19789 mr = 40584 m= 2759 mr = 14241 m= 109 mr = 1589 m= 2 mr = 25 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 0.4300000 number of dielectric boundary points 26054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 16354 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) : 0.6115683 object centre at (A) : 5.711500 24.46350 24.03750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2055302E-03 -2.4600158E-02 midg,1,midg; midg,igrid,midg -3.7315357E-02 -3.8810752E-02 1,midg,midg; igrid,midg,midg -9.1623869E-03 1.5715605E-02 gauss-seidel spectral radius is 0.9984916 estimated iterations to convergence 204 setup time was (sec) 0.6900000 now iterating at: 03:35:34 rms-change max change #iterations 3.594573 170.6175 at 10iterations 1.611510 65.19025 at 20iterations 0.7269823 28.96283 at 30iterations 0.3270754 12.90301 at 40iterations 0.1472667 5.329274 at 50iterations 6.6438727E-02 2.578445 at 60iterations 2.9807949E-02 1.095181 at 70iterations 1.3429071E-02 0.4804754 at 80iterations 6.0731727E-03 0.2185812 at 90iterations 2.7167737E-03 9.6956253E-02 at 100iterations 1.2256041E-03 4.2869568E-02 at 110iterations 5.5296312E-04 2.0335197E-02 at 120iterations finished qdiffx linear iterations at : 03:35:40 total time elapsed so far: 6.610000 # loops : 120 mean,max change (kT/e) : 5.5296312E-04 2.0335197E-02 energy calculations done at 6.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.780000 DelPhi exited at 03:35:41 6.781u 0.170s 0:08.43 82.4% 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 03:35:42 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2186 !!! WARNING: ASL 331 has a net charge of -0.1000 !!! WARNING: HIR 435 has a net charge of 0.5140 !!! WARNING: GLU 460 has a net charge of -2.0000 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: 2.752057 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): -15.56700 26.99000 ymin,ymax (A): -2.479000 51.40600 zmin,zma (A): -5.068000 53.14300 x,y,z range (A): 42.55700 53.88500 58.21100 scale (grids/A): 2.752057 object centre (A): 5.711500 24.46350 24.03750 number of atom coordinates read : 2186 total number of charged atoms : 2088 net assigned charge : -6.585979 assigned positive charge : 323.1335 centred at (gu) : 86.23930 87.38995 86.10731 assigned negative charge : -329.7199 centred at (gu) : 85.55078 87.88275 86.21895 start vw surface at 0.1400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 138736 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19782 grid for indexing accessible points = 1.400000 m= 65935 mr = 99130 m= 22306 mr = 53101 m= 4711 mr = 17496 m= 508 mr = 3415 m= 13 mr = 298 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.5800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.030000 number of dielectric boundary points 58767 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 16701 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) : 1.834705 object centre at (A) : 5.711500 24.46350 24.03750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2375294E-02 -0.3307794 midg,1,midg; midg,igrid,midg -0.4025848 -0.4758421 1,midg,midg; igrid,midg,midg -5.9637178E-02 0.2186627 gauss-seidel spectral radius is 0.9992155 estimated iterations to convergence 282 setup time was (sec) 1.320000 now iterating at: 03:35:43 rms-change max change #iterations 8.579060 276.7395 at 10iterations 4.885413 114.2870 at 20iterations 2.765811 62.42162 at 30iterations 1.560583 34.36800 at 40iterations 0.8835294 18.23738 at 50iterations 0.4969891 10.21358 at 60iterations 0.2809684 6.189332 at 70iterations 0.1581521 3.054627 at 80iterations 8.9145482E-02 2.053653 at 90iterations 5.0281599E-02 0.9907923 at 100iterations 2.8309103E-02 0.5389252 at 110iterations 1.5984287E-02 0.3365660 at 120iterations 8.9965528E-03 0.1932154 at 130iterations 5.0712153E-03 0.1043358 at 140iterations 2.8627038E-03 5.5042267E-02 at 150iterations 1.6119579E-03 3.7094116E-02 at 160iterations 9.0819533E-04 1.8630505E-02 at 170iterations 5.1380997E-04 1.0795593E-02 at 180iterations finished qdiffx linear iterations at : 03:35:54 total time elapsed so far: 11.85000 # loops : 180 mean,max change (kT/e) : 5.1380997E-04 1.0795593E-02 energy calculations done at 11.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 03:35:54 12.034u 0.204s 0:12.71 96.2% 0+0k 0+0io 0pf+0w