Mon Oct 10 09:22:32 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 09:22:32 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 0.6120414 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): -9.045000 49.12100 ymin,ymax (A): 8.866000 47.49900 zmin,zma (A): -3.624000 38.90800 x,y,z range (A): 58.16600 38.63300 42.53200 scale (grids/A): 0.6120414 object centre (A): 20.03800 28.18250 17.64200 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000011 assigned positive charge : 292.6019 centred at (gu) : 90.12105 89.72375 90.47860 assigned negative charge : -287.6023 centred at (gu) : 90.09850 89.63967 90.58889 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4944 nv = 96 ne = 84 npr = 40081 no. pairs analyzed = 40081 no. exposed pairs = 2487 no. arc points = 17397 no. surface atoms = 840 nbur = 1126 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 215 mr = 2682 m= 2 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2464 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1806 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6012 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.6832953E-09 -1.3264468E-09 midg,1,midg; midg,igrid,midg -1.4544463E-10 6.0499228E-09 1,midg,midg; igrid,midg,midg 2.2440552E-09 4.1694697E-09 gauss-seidel spectral radius is 0.9861247 estimated iterations to convergence 70 setup time was (sec) 0.4600000 now iterating at: 09:22:33 rms-change max change #iterations 0.1075058 22.00326 at 10iterations 9.5706023E-03 1.902860 at 20iterations 8.4578409E-04 0.1455708 at 30iterations 7.3745636E-05 1.2314796E-02 at 40iterations 6.5890245E-06 1.1610985E-03 at 50iterations finished qdiffx linear iterations at : 09:22:35 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 6.5890245E-06 1.1610985E-03 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 09:22:36 3.137u 0.146s 0:03.56 91.8% 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 09:22:36 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 1.836124 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): -9.045000 49.12100 ymin,ymax (A): 8.866000 47.49900 zmin,zma (A): -3.624000 38.90800 x,y,z range (A): 58.16600 38.63300 42.53200 scale (grids/A): 1.836124 object centre (A): 20.03800 28.18250 17.64200 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000011 assigned positive charge : 292.6019 centred at (gu) : 90.36314 89.17131 91.43557 assigned negative charge : -287.6023 centred at (gu) : 90.29566 88.91929 91.76697 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 53626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17397 grid for indexing accessible points = 1.400000 m= 17872 mr = 36501 m= 2208 mr = 13240 m= 78 mr = 1288 m= 0 mr = 17 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 1451 time to turn everything in is 0.3800000 number of dielectric boundary points 22738 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 14360 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) : 0.6120414 object centre at (A) : 20.03800 28.18250 17.64200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0427627E-02 -1.6728889E-03 midg,1,midg; midg,igrid,midg 1.5137891E-03 8.0309073E-03 1,midg,midg; igrid,midg,midg 3.1039700E-02 4.0946260E-02 gauss-seidel spectral radius is 0.9984565 estimated iterations to convergence 202 setup time was (sec) 0.6600000 now iterating at: 09:22:37 rms-change max change #iterations 3.379541 142.9261 at 10iterations 1.499537 71.20257 at 20iterations 0.6700053 24.25795 at 30iterations 0.2986561 12.35181 at 40iterations 0.1340449 5.153067 at 50iterations 5.9501804E-02 2.122654 at 60iterations 2.6608868E-02 0.9716936 at 70iterations 1.1862195E-02 0.4777451 at 80iterations 5.2872719E-03 0.2115264 at 90iterations 2.3618808E-03 0.1042881 at 100iterations 1.0536668E-03 4.5463562E-02 at 110iterations 4.7001522E-04 1.7517090E-02 at 120iterations finished qdiffx linear iterations at : 09:22:43 total time elapsed so far: 6.710000 # loops : 120 mean,max change (kT/e) : 4.7001522E-04 1.7517090E-02 energy calculations done at 6.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 09:22:43 6.894u 0.169s 0:07.33 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 09:22:43 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 2.754186 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): -9.045000 49.12100 ymin,ymax (A): 8.866000 47.49900 zmin,zma (A): -3.624000 38.90800 x,y,z range (A): 58.16600 38.63300 42.53200 scale (grids/A): 2.754186 object centre (A): 20.03800 28.18250 17.64200 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000011 assigned positive charge : 292.6019 centred at (gu) : 90.54482 88.75690 92.15339 assigned negative charge : -287.6023 centred at (gu) : 90.44353 88.37894 92.65051 start vw surface at 0.1200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 124430 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17397 grid for indexing accessible points = 1.400000 m= 59471 mr = 88966 m= 19387 mr = 48704 m= 3815 mr = 15530 m= 325 mr = 2801 m= 7 mr = 206 m= 0 mr = 2 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 5084 time to turn everything in is 0.9000000 number of dielectric boundary points 51226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.020000 number of grid points assigned charge 14672 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) : 1.836124 object centre at (A) : 20.03800 28.18250 17.64200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9902314E-02 4.1129119E-03 midg,1,midg; midg,igrid,midg 4.6253730E-02 6.9867209E-02 1,midg,midg; igrid,midg,midg 0.3687836 0.4910742 gauss-seidel spectral radius is 0.9991909 estimated iterations to convergence 278 setup time was (sec) 1.180000 now iterating at: 09:22:45 rms-change max change #iterations 8.015632 317.4129 at 10iterations 4.542491 126.0942 at 20iterations 2.564788 59.65355 at 30iterations 1.436393 33.06225 at 40iterations 0.8058649 18.01987 at 50iterations 0.4506620 10.10400 at 60iterations 0.2526858 5.391865 at 70iterations 0.1411753 3.205750 at 80iterations 7.8971483E-02 1.706779 at 90iterations 4.4210974E-02 0.9985771 at 100iterations 2.4717748E-02 0.5331764 at 110iterations 1.3811690E-02 0.3246784 at 120iterations 7.7207424E-03 0.1682992 at 130iterations 4.3233391E-03 9.1709137E-02 at 140iterations 2.4170310E-03 5.0156116E-02 at 150iterations 1.3468218E-03 2.7331084E-02 at 160iterations 7.5408892E-04 1.6967773E-02 at 170iterations 4.2183301E-04 8.4991455E-03 at 180iterations finished qdiffx linear iterations at : 09:22:54 total time elapsed so far: 10.58000 # loops : 180 mean,max change (kT/e) : 4.2183301E-04 8.4991455E-03 energy calculations done at 10.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.76000 DelPhi exited at 09:22:55 10.763u 0.211s 0:11.28 97.2% 0+0k 0+0io 0pf+0w