Mon Oct 10 10:29:08 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+sph.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 = amb.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 10:29:08 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: 385 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3571 !!! WARNING: MG1 1012 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5873522 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): 36.04800 86.24900 ymin,ymax (A): 25.68100 85.93200 zmin,zma (A): -93.14200 -32.53100 x,y,z range (A): 50.20100 60.25100 60.61100 scale (grids/A): 0.5873522 object centre (A): 61.14850 55.80650 -62.83650 number of atom coordinates read : 3571 total number of charged atoms : 2990 net assigned charge : 17.90001 assigned positive charge : 465.1382 centred at (gu) : 91.74678 89.34766 88.99837 assigned negative charge : -447.2395 centred at (gu) : 91.81509 89.30402 88.89033 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8265 nv = 96 ne = 84 npr = 72298 no. pairs analyzed = 72298 no. exposed pairs = 5221 no. arc points = 36502 no. surface atoms = 1731 nbur = 1840 mkacc time = 0.1800000 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= 457 mr = 3947 m= 4 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 50 time to turn everything in is 0.4100000 number of dielectric boundary points 4739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3075 ## 333 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 9131 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4957545E-09 6.4393997E-09 midg,1,midg; midg,igrid,midg 4.4651887E-09 5.4474256E-09 1,midg,midg; igrid,midg,midg 4.7208664E-09 4.6404955E-09 gauss-seidel spectral radius is 0.9851040 estimated iterations to convergence 67 setup time was (sec) 0.6600000 now iterating at: 10:29:09 rms-change max change #iterations 0.1095338 15.48788 at 10iterations 9.0829916E-03 1.656646 at 20iterations 8.5193134E-04 0.1232834 at 30iterations 1.5724861E-04 2.6100159E-02 at 40iterations 4.3743003E-05 8.0642700E-03 at 50iterations finished qdiffx linear iterations at : 10:29:12 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 4.3743003E-05 8.0642700E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.720000 DelPhi exited at 10:29:13 3.722u 0.217s 0:04.79 82.0% 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 10:29:13 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: 385 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3571 !!! WARNING: MG1 1012 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.762056 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): 36.04800 86.24900 ymin,ymax (A): 25.68100 85.93200 zmin,zma (A): -93.14200 -32.53100 x,y,z range (A): 50.20100 60.25100 60.61100 scale (grids/A): 1.762056 object centre (A): 61.14850 55.80650 -62.83650 number of atom coordinates read : 3571 total number of charged atoms : 2990 net assigned charge : 17.90001 assigned positive charge : 465.1382 centred at (gu) : 95.23951 88.04198 86.99423 assigned negative charge : -447.2395 centred at (gu) : 95.44520 87.91200 86.67075 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 88875 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36502 grid for indexing accessible points = 1.400000 m= 29620 mr = 56574 m= 4393 mr = 20113 m= 167 mr = 2402 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 405 time to turn everything in is 0.6700000 number of dielectric boundary points 43937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 245 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 23252 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) : 0.5873522 object centre at (A) : 61.14850 55.80650 -62.83650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3284429E-02 2.3489907E-02 midg,1,midg; midg,igrid,midg 4.1476093E-02 4.2455290E-02 1,midg,midg; igrid,midg,midg 2.0207036E-02 1.0717935E-02 gauss-seidel spectral radius is 0.9985404 estimated iterations to convergence 208 setup time was (sec) 0.9900000 now iterating at: 10:29:14 rms-change max change #iterations 4.040347 172.5495 at 10iterations 1.836533 71.73427 at 20iterations 0.8361384 28.25992 at 30iterations 0.3803760 12.45792 at 40iterations 0.1738226 5.679973 at 50iterations 7.9216793E-02 2.418694 at 60iterations 3.6047701E-02 1.090983 at 70iterations 1.6494023E-02 0.5736713 at 80iterations 7.5257919E-03 0.2311797 at 90iterations 3.4354108E-03 0.1163216 at 100iterations 1.5680365E-03 4.7073364E-02 at 110iterations 7.1708683E-04 2.0412445E-02 at 120iterations finished qdiffx linear iterations at : 10:29:21 total time elapsed so far: 8.040000 # loops : 120 mean,max change (kT/e) : 7.1708683E-04 2.0412445E-02 energy calculations done at 8.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.240000 DelPhi exited at 10:29:22 8.241u 0.236s 0:08.87 95.4% 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 Mon Oct 10 2011 at 10:29:22 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: 385 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3571 !!! WARNING: MG1 1012 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= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.643085 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): 36.04800 86.24900 ymin,ymax (A): 25.68100 85.93200 zmin,zma (A): -93.14200 -32.53100 x,y,z range (A): 50.20100 60.25100 60.61100 scale (grids/A): 2.643085 object centre (A): 61.14850 55.80650 -62.83650 number of atom coordinates read : 3571 total number of charged atoms : 2990 net assigned charge : 17.90001 assigned positive charge : 465.1382 centred at (gu) : 97.85913 87.06286 85.49130 assigned negative charge : -447.2395 centred at (gu) : 98.16778 86.86798 85.00589 start vw surface at 0.2400000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 205635 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36502 grid for indexing accessible points = 1.400000 m= 96317 mr = 139079 m= 32919 mr = 74281 m= 7495 mr = 24948 m= 825 mr = 5290 m= 21 mr = 458 m= 0 mr = 3 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 1436 time to turn everything in is 1.700000 number of dielectric boundary points 99153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 23912 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) : 1.762056 object centre at (A) : 61.14850 55.80650 -62.83650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1370681E-02 0.3057418 midg,1,midg; midg,igrid,midg 0.6431878 0.4020270 1,midg,midg; igrid,midg,midg 0.2443383 4.9313709E-02 gauss-seidel spectral radius is 0.9992775 estimated iterations to convergence 294 setup time was (sec) 2.020000 now iterating at: 10:29:24 rms-change max change #iterations 10.01803 272.6113 at 10iterations 5.993440 162.1859 at 20iterations 3.531102 81.25523 at 30iterations 2.078555 40.37984 at 40iterations 1.216773 26.22260 at 50iterations 0.7127376 14.12310 at 60iterations 0.4139325 7.992093 at 70iterations 0.2411049 4.965769 at 80iterations 0.1400569 2.745043 at 90iterations 8.1393845E-02 1.512363 at 100iterations 4.7210127E-02 0.8834081 at 110iterations 2.7389806E-02 0.5665359 at 120iterations 1.5855007E-02 0.2773495 at 130iterations 9.1721062E-03 0.1616030 at 140iterations 5.3173904E-03 0.1016197 at 150iterations 3.0832731E-03 5.7451248E-02 at 160iterations 1.7777050E-03 3.1671047E-02 at 170iterations 1.0306805E-03 1.9603729E-02 at 180iterations finished qdiffx linear iterations at : 10:29:35 total time elapsed so far: 12.36000 # loops : 180 mean,max change (kT/e) : 1.0306805E-03 1.9603729E-02 energy calculations done at 12.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 10:29:35 12.557u 0.171s 0:13.06 97.3% 0+0k 0+0io 0pf+0w