Mon Oct 10 17:07:00 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 Mon Oct 10 2011 at 17:07:00 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 = 2589 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 0.5568852 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): -2.251000 40.13700 ymin,ymax (A): -9.385000 41.87600 zmin,zma (A): -1.263000 62.66400 x,y,z range (A): 42.38800 51.26100 63.92700 scale (grids/A): 0.5568852 object centre (A): 18.94300 16.24550 30.70050 number of atom coordinates read : 2589 total number of charged atoms : 2449 net assigned charge : 7.906022 assigned positive charge : 382.9467 centred at (gu) : 89.47716 89.29641 89.46311 assigned negative charge : -375.0417 centred at (gu) : 89.55445 89.19524 89.50336 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5287 nv = 96 ne = 84 npr = 51304 no. pairs analyzed = 51304 no. exposed pairs = 3481 no. arc points = 24549 no. surface atoms = 1166 nbur = 1423 mkacc time = 0.1400000 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 = 1.540000 m= 245 mr = 2585 m= 0 mr = 12 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 2935 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2542 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 6839 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2333645E-09 3.6442954E-10 midg,1,midg; midg,igrid,midg -1.3484382E-10 1.3377169E-09 1,midg,midg; igrid,midg,midg 1.5765712E-09 8.9460661E-11 gauss-seidel spectral radius is 0.9833432 estimated iterations to convergence 64 setup time was (sec) 0.6200000 now iterating at: 17:07:00 rms-change max change #iterations 7.5848117E-02 15.11317 at 10iterations 5.2625453E-03 1.061020 at 20iterations 3.8502630E-04 6.0974121E-02 at 30iterations 3.0831281E-05 5.0048828E-03 at 40iterations 3.0991307E-06 4.8398972E-04 at 50iterations finished qdiffx linear iterations at : 17:07:04 total time elapsed so far: 4.040000 # loops : 50 mean,max change (kT/e) : 3.0991307E-06 4.8398972E-04 energy calculations done at 4.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.220000 DelPhi exited at 17:07:05 4.223u 0.249s 0:04.90 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 Mon Oct 10 2011 at 17:07:05 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 = 2589 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 1.670655 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): -2.251000 40.13700 ymin,ymax (A): -9.385000 41.87600 zmin,zma (A): -1.263000 62.66400 x,y,z range (A): 42.38800 51.26100 63.92700 scale (grids/A): 1.670655 object centre (A): 18.94300 16.24550 30.70050 number of atom coordinates read : 2589 total number of charged atoms : 2449 net assigned charge : 7.906022 assigned positive charge : 382.9467 centred at (gu) : 88.43090 87.88863 88.38887 assigned negative charge : -375.0417 centred at (gu) : 88.66318 87.58539 88.51008 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 58314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24549 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18785 mr = 38410 m= 2107 mr = 12816 m= 58 mr = 1027 m= 1 mr = 1 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 198 time to turn everything in is 0.5400000 number of dielectric boundary points 27012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 238 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 18831 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) : 0.5568852 object centre at (A) : 18.94300 16.24550 30.70050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9389180E-02 2.2787351E-02 midg,1,midg; midg,igrid,midg -7.5017544E-03 8.8858735E-03 1,midg,midg; igrid,midg,midg 1.0940732E-02 3.6158555E-04 gauss-seidel spectral radius is 0.9982324 estimated iterations to convergence 189 setup time was (sec) 0.9000000 now iterating at: 17:07:06 rms-change max change #iterations 3.193733 155.0280 at 10iterations 1.338976 51.17974 at 20iterations 0.5632607 23.36832 at 30iterations 0.2377278 8.566648 at 40iterations 9.9907987E-02 3.795402 at 50iterations 4.2143703E-02 1.637511 at 60iterations 1.7750012E-02 0.7624588 at 70iterations 7.4906899E-03 0.2904835 at 80iterations 3.1553097E-03 0.1317139 at 90iterations 1.3293257E-03 5.0980568E-02 at 100iterations 5.6138064E-04 2.3197174E-02 at 110iterations 2.3805849E-04 1.0021210E-02 at 120iterations finished qdiffx linear iterations at : 17:07:14 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 2.3805849E-04 1.0021210E-02 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.530000 DelPhi exited at 17:07:15 9.532u 0.238s 0:10.15 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 Mon Oct 10 2011 at 17:07:15 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 = 2589 !!! WARNING: GLM 155 has a net charge of -0.0940 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: 2.505983 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): -2.251000 40.13700 ymin,ymax (A): -9.385000 41.87600 zmin,zma (A): -1.263000 62.66400 x,y,z range (A): 42.38800 51.26100 63.92700 scale (grids/A): 2.505983 object centre (A): 18.94300 16.24550 30.70050 number of atom coordinates read : 2589 total number of charged atoms : 2449 net assigned charge : 7.906022 assigned positive charge : 382.9467 centred at (gu) : 87.64615 86.83272 87.58306 assigned negative charge : -375.0417 centred at (gu) : 87.99471 86.37804 87.76517 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 134947 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24549 grid for indexing accessible points = 1.400000 m= 63034 mr = 93899 m= 19333 mr = 49481 m= 3352 mr = 14454 m= 204 mr = 2125 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 650 time to turn everything in is 1.180000 number of dielectric boundary points 60851 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 19574 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) : 1.670655 object centre at (A) : 18.94300 16.24550 30.70050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2267944 0.5780206 midg,1,midg; midg,igrid,midg -7.0140980E-02 0.1493208 1,midg,midg; igrid,midg,midg 0.1305142 -8.3303759E-03 gauss-seidel spectral radius is 0.9991516 estimated iterations to convergence 271 setup time was (sec) 1.510000 now iterating at: 17:07:17 rms-change max change #iterations 8.295631 319.7172 at 10iterations 4.709155 139.2205 at 20iterations 2.644078 64.55332 at 30iterations 1.475315 42.90710 at 40iterations 0.8249324 20.50947 at 50iterations 0.4585778 10.75430 at 60iterations 0.2539009 6.322747 at 70iterations 0.1408603 3.223480 at 80iterations 7.7836037E-02 1.955133 at 90iterations 4.3027822E-02 1.021372 at 100iterations 2.3789160E-02 0.4800148 at 110iterations 1.3161115E-02 0.2813148 at 120iterations 7.2605284E-03 0.1691798 at 130iterations 4.0187752E-03 9.0103149E-02 at 140iterations 2.2175210E-03 4.7332764E-02 at 150iterations 1.2179227E-03 2.6039124E-02 at 160iterations 6.7251665E-04 1.4545381E-02 at 170iterations 3.7164794E-04 8.6410046E-03 at 180iterations finished qdiffx linear iterations at : 17:07:30 total time elapsed so far: 15.29000 # loops : 180 mean,max change (kT/e) : 3.7164794E-04 8.6410046E-03 energy calculations done at 15.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.51000 DelPhi exited at 17:07:31 15.514u 0.304s 0:16.18 97.7% 0+0k 0+0io 0pf+0w