Sat Oct 8 17:18:59 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 Sat Oct 8 2011 at 17:18:59 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3732 !!! WARNING: ASL 237 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5456775 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): -27.99900 33.43200 ymin,ymax (A): -33.95000 31.29000 zmin,zma (A): 9.606000 63.28000 x,y,z range (A): 61.43100 65.24000 53.67400 scale (grids/A): 0.5456775 object centre (A): 2.716499 -1.330001 36.44300 number of atom coordinates read : 3732 total number of charged atoms : 3583 net assigned charge : -8.099966 assigned positive charge : 573.2596 centred at (gu) : 88.97003 90.32569 90.44139 assigned negative charge : -581.3619 centred at (gu) : 89.04173 90.31773 90.44713 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7043 nv = 96 ne = 84 npr = 76744 no. pairs analyzed = 76744 no. exposed pairs = 4538 no. arc points = 31394 no. surface atoms = 1517 nbur = 2215 mkacc time = 0.1600000 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 = 1.568000 m= 280 mr = 3798 m= 0 mr = 11 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3800000 number of dielectric boundary points 3514 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3169 ## 403 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9347 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1015891E-10 -6.1672606E-10 midg,1,midg; midg,igrid,midg -5.2998700E-10 -4.7200516E-10 1,midg,midg; igrid,midg,midg 1.4443530E-10 -8.7476004E-10 gauss-seidel spectral radius is 0.9827351 estimated iterations to convergence 63 setup time was (sec) 0.5900000 now iterating at: 17:18:59 rms-change max change #iterations 8.5439004E-02 13.57180 at 10iterations 5.6235003E-03 0.8310934 at 20iterations 3.8792202E-04 5.6177139E-02 at 30iterations 3.2646851E-05 4.9018860E-03 at 40iterations 5.4430188E-06 9.4985962E-04 at 50iterations finished qdiffx linear iterations at : 17:19:02 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 5.4430188E-06 9.4985962E-04 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 17:19:02 3.175u 0.157s 0:03.69 89.9% 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 Sat Oct 8 2011 at 17:19:02 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3732 !!! WARNING: ASL 237 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.637033 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): -27.99900 33.43200 ymin,ymax (A): -33.95000 31.29000 zmin,zma (A): 9.606000 63.28000 x,y,z range (A): 61.43100 65.24000 53.67400 scale (grids/A): 1.637033 object centre (A): 2.716499 -1.330001 36.44300 number of atom coordinates read : 3732 total number of charged atoms : 3583 net assigned charge : -8.099966 assigned positive charge : 573.2596 centred at (gu) : 86.90881 90.97597 91.32284 assigned negative charge : -581.3619 centred at (gu) : 87.12462 90.95300 91.34095 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 78083 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31394 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 25096 mr = 54376 m= 2701 mr = 17531 m= 97 mr = 1439 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1926 time to turn everything in is 0.5400000 number of dielectric boundary points 32615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 373 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 27443 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) : 0.5456775 object centre at (A) : 2.716499 -1.330001 36.44300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7670903E-03 -9.0057980E-03 midg,1,midg; midg,igrid,midg -2.8238799E-03 1.4221980E-03 1,midg,midg; igrid,midg,midg -1.7640902E-02 -2.9309558E-02 gauss-seidel spectral radius is 0.9982596 estimated iterations to convergence 190 setup time was (sec) 0.8100000 now iterating at: 17:19:03 rms-change max change #iterations 3.886399 177.2440 at 10iterations 1.652396 72.46399 at 20iterations 0.6993638 26.77700 at 30iterations 0.2972718 10.98263 at 40iterations 0.1263454 4.109449 at 50iterations 5.3787313E-02 1.840711 at 60iterations 2.2835230E-02 0.7829018 at 70iterations 9.7119678E-03 0.3458385 at 80iterations 4.1534924E-03 0.1317101 at 90iterations 1.7639678E-03 5.6919098E-02 at 100iterations 7.5106125E-04 2.6634216E-02 at 110iterations 3.2313410E-04 1.0263443E-02 at 120iterations finished qdiffx linear iterations at : 17:19:09 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 3.2313410E-04 1.0263443E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 17:19:10 7.001u 0.168s 0:07.45 96.1% 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 Sat Oct 8 2011 at 17:19:10 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3732 !!! WARNING: ASL 237 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.455549 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): -27.99900 33.43200 ymin,ymax (A): -33.95000 31.29000 zmin,zma (A): 9.606000 63.28000 x,y,z range (A): 61.43100 65.24000 53.67400 scale (grids/A): 2.455549 object centre (A): 2.716499 -1.330001 36.44300 number of atom coordinates read : 3732 total number of charged atoms : 3583 net assigned charge : -8.099966 assigned positive charge : 573.2596 centred at (gu) : 85.36297 91.46363 91.98407 assigned negative charge : -581.3619 centred at (gu) : 85.68684 91.42951 92.01138 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 181709 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31394 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 86247 mr = 132751 m= 25084 mr = 68925 m= 4314 mr = 19223 m= 369 mr = 2875 m= 6 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 6889 time to turn everything in is 1.300000 number of dielectric boundary points 73777 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 28625 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) : 1.637033 object centre at (A) : 2.716499 -1.330001 36.44300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.4125302E-02 -0.1433343 midg,1,midg; midg,igrid,midg -2.3087541E-02 8.3939835E-02 1,midg,midg; igrid,midg,midg -0.4172190 -0.4077007 gauss-seidel spectral radius is 0.9991715 estimated iterations to convergence 274 setup time was (sec) 1.590000 now iterating at: 17:19:12 rms-change max change #iterations 9.992172 292.7257 at 10iterations 5.661344 119.3337 at 20iterations 3.203232 71.55367 at 30iterations 1.796733 38.61452 at 40iterations 1.009065 21.54379 at 50iterations 0.5651489 11.10100 at 60iterations 0.3153307 6.547203 at 70iterations 0.1763762 3.256741 at 80iterations 9.8256446E-02 1.871431 at 90iterations 5.4867845E-02 1.077797 at 100iterations 3.0532762E-02 0.5901680 at 110iterations 1.7037667E-02 0.3119392 at 120iterations 9.4878012E-03 0.1671224 at 130iterations 5.2805902E-03 9.8514557E-02 at 140iterations 2.9363509E-03 5.4029465E-02 at 150iterations 1.6374612E-03 2.9255390E-02 at 160iterations 9.1306283E-04 1.7033577E-02 at 170iterations 5.1131670E-04 9.1629028E-03 at 180iterations finished qdiffx linear iterations at : 17:19:21 total time elapsed so far: 11.28000 # loops : 180 mean,max change (kT/e) : 5.1131670E-04 9.1629028E-03 energy calculations done at 11.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.45000 DelPhi exited at 17:19:22 11.451u 0.206s 0:11.93 97.6% 0+0k 0+0io 0pf+0w