Mon Oct 10 10:20:44 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 10:20:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5771538 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): 16.29900 75.06300 ymin,ymax (A): -45.00000 6.076000 zmin,zma (A): 9.735000 71.41700 x,y,z range (A): 58.76400 51.07600 61.68200 scale (grids/A): 0.5771538 object centre (A): 45.68100 -19.46200 40.57600 number of atom coordinates read : 2896 total number of charged atoms : 2746 net assigned charge : 8.000022 assigned positive charge : 422.7878 centred at (gu) : 92.21560 89.33972 88.79928 assigned negative charge : -414.7883 centred at (gu) : 92.46308 89.39532 88.71101 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6572 nv = 96 ne = 84 npr = 55245 no. pairs analyzed = 55245 no. exposed pairs = 4530 no. arc points = 32671 no. surface atoms = 1488 nbur = 1408 mkacc time = 0.1000000 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= 322 mr = 2798 m= 0 mr = 10 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 4086 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3212 ## 393 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8226 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.3971510E-11 2.5138907E-09 midg,1,midg; midg,igrid,midg 3.1825174E-09 5.8327621E-10 1,midg,midg; igrid,midg,midg 3.6708077E-09 -5.2340701E-09 gauss-seidel spectral radius is 0.9845228 estimated iterations to convergence 66 setup time was (sec) 0.4100000 now iterating at: 10:20:44 rms-change max change #iterations 9.2546374E-02 16.38212 at 10iterations 7.0701661E-03 1.264709 at 20iterations 5.5220490E-04 8.6917877E-02 at 30iterations 5.1865100E-05 1.1095047E-02 at 40iterations 8.1572798E-06 1.4476776E-03 at 50iterations finished qdiffx linear iterations at : 10:20:47 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 8.1572798E-06 1.4476776E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 10:20:48 3.463u 0.166s 0:03.96 91.4% 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 10:20:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 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: 1.731461 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): 16.29900 75.06300 ymin,ymax (A): -45.00000 6.076000 zmin,zma (A): 9.735000 71.41700 x,y,z range (A): 58.76400 51.07600 61.68200 scale (grids/A): 1.731461 object centre (A): 45.68100 -19.46200 40.57600 number of atom coordinates read : 2896 total number of charged atoms : 2746 net assigned charge : 8.000022 assigned positive charge : 422.7878 centred at (gu) : 96.64612 88.01855 86.39716 assigned negative charge : -414.7883 centred at (gu) : 97.38893 88.18581 86.13292 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69487 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32671 grid for indexing accessible points = 1.400000 m= 22264 mr = 41330 m= 2954 mr = 14055 m= 119 mr = 1372 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 38054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 275 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21273 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) : 0.5771538 object centre at (A) : 45.68100 -19.46200 40.57600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5040134E-03 3.9445899E-02 midg,1,midg; midg,igrid,midg 8.2743363E-03 1.0483998E-02 1,midg,midg; igrid,midg,midg 2.6439480E-02 1.5754120E-04 gauss-seidel spectral radius is 0.9984116 estimated iterations to convergence 199 setup time was (sec) 0.5800000 now iterating at: 10:20:48 rms-change max change #iterations 3.631388 182.0868 at 10iterations 1.585123 58.19142 at 20iterations 0.6983135 26.61051 at 30iterations 0.3052548 10.09659 at 40iterations 0.1344295 5.006393 at 50iterations 5.9090357E-02 2.248291 at 60iterations 2.5892358E-02 0.8711944 at 70iterations 1.1348720E-02 0.4128437 at 80iterations 5.0300788E-03 0.1718869 at 90iterations 2.2005667E-03 7.8590393E-02 at 100iterations 9.6842676E-04 3.5349846E-02 at 110iterations 4.2734767E-04 1.4401436E-02 at 120iterations finished qdiffx linear iterations at : 10:20:56 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 4.2734767E-04 1.4401436E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 10:20:56 7.957u 0.198s 0:08.55 95.2% 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 10:20:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2896 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.597192 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): 16.29900 75.06300 ymin,ymax (A): -45.00000 6.076000 zmin,zma (A): 9.735000 71.41700 x,y,z range (A): 58.76400 51.07600 61.68200 scale (grids/A): 2.597192 object centre (A): 45.68100 -19.46200 40.57600 number of atom coordinates read : 2896 total number of charged atoms : 2746 net assigned charge : 8.000022 assigned positive charge : 422.7878 centred at (gu) : 99.96909 87.02764 84.59559 assigned negative charge : -414.7883 centred at (gu) : 101.0833 87.27852 84.19919 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 160330 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32671 grid for indexing accessible points = 1.400000 m= 72233 mr = 102429 m= 24310 mr = 53197 m= 4826 mr = 17473 m= 442 mr = 2980 m= 24 mr = 177 m= 0 mr = 4 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8900000 number of dielectric boundary points 85905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 0.9800000 number of grid points assigned charge 21955 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) : 1.731461 object centre at (A) : 45.68100 -19.46200 40.57600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0912196E-02 0.7815537 midg,1,midg; midg,igrid,midg 7.4307839E-03 0.1234588 1,midg,midg; igrid,midg,midg 0.4030073 4.9863774E-03 gauss-seidel spectral radius is 0.9992263 estimated iterations to convergence 284 setup time was (sec) 1.120000 now iterating at: 10:20:58 rms-change max change #iterations 9.416709 303.0401 at 10iterations 5.559700 190.5190 at 20iterations 3.237901 81.36195 at 30iterations 1.874979 45.02606 at 40iterations 1.077349 25.07186 at 50iterations 0.6196065 14.84549 at 60iterations 0.3544405 7.787111 at 70iterations 0.2029426 4.982083 at 80iterations 0.1156086 2.395350 at 90iterations 6.5871283E-02 1.433244 at 100iterations 3.7475519E-02 0.8560057 at 110iterations 2.1292653E-02 0.4579353 at 120iterations 1.2115235E-02 0.2706847 at 130iterations 6.8720980E-03 0.1507320 at 140iterations 3.9026069E-03 8.6057663E-02 at 150iterations 2.2174756E-03 4.3964386E-02 at 160iterations 1.2597138E-03 2.5203705E-02 at 170iterations 7.1464019E-04 1.4219701E-02 at 180iterations finished qdiffx linear iterations at : 10:21:09 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 7.1464019E-04 1.4219701E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 10:21:10 12.815u 0.207s 0:13.29 97.8% 0+0k 0+0io 0pf+0w