Sat Oct 8 17:44:39 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 Sat Oct 8 2011 at 17:44:39 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 = 3421 !!! WARNING: GLN 381 has a net charge of -0.2720 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: 0.6012904 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): -8.019000 51.18700 ymin,ymax (A): 15.35100 70.59500 zmin,zma (A): 12.96400 70.98300 x,y,z range (A): 59.20600 55.24400 58.01900 scale (grids/A): 0.6012904 object centre (A): 21.58400 42.97300 41.97350 number of atom coordinates read : 3421 total number of charged atoms : 3275 net assigned charge : -5.771983 assigned positive charge : 511.8365 centred at (gu) : 87.72150 88.07945 88.33217 assigned negative charge : -517.6097 centred at (gu) : 87.68285 88.09370 88.32303 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8265 nv = 96 ne = 84 npr = 69224 no. pairs analyzed = 69224 no. exposed pairs = 4272 no. arc points = 29575 no. surface atoms = 1448 nbur = 1973 mkacc time = 0.1200000 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 = 1.456000 m= 412 mr = 4521 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2500000 number of dielectric boundary points 4119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3060 ## 301 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 10346 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.2888137E-09 -1.4311394E-09 midg,1,midg; midg,igrid,midg -2.7127922E-09 -2.1106856E-09 1,midg,midg; igrid,midg,midg -7.4482891E-09 -3.8569134E-10 gauss-seidel spectral radius is 0.9857524 estimated iterations to convergence 69 setup time was (sec) 0.4600000 now iterating at: 17:44:40 rms-change max change #iterations 0.1244665 16.67637 at 10iterations 1.0861117E-02 1.466179 at 20iterations 1.0017582E-03 0.1362538 at 30iterations 1.3315929E-04 1.8210411E-02 at 40iterations 3.1394044E-05 4.6505928E-03 at 50iterations finished qdiffx linear iterations at : 17:44:43 total time elapsed so far: 3.560000 # loops : 50 mean,max change (kT/e) : 3.1394044E-05 4.6505928E-03 energy calculations done at 3.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 17:44:43 3.694u 0.212s 0:04.18 93.3% 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 17:44:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3421 !!! WARNING: GLN 381 has a net charge of -0.2720 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: 1.803871 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): -8.019000 51.18700 ymin,ymax (A): 15.35100 70.59500 zmin,zma (A): 12.96400 70.98300 x,y,z range (A): 59.20600 55.24400 58.01900 scale (grids/A): 1.803871 object centre (A): 21.58400 42.97300 41.97350 number of atom coordinates read : 3421 total number of charged atoms : 3275 net assigned charge : -5.771983 assigned positive charge : 511.8365 centred at (gu) : 83.16360 84.23723 84.99558 assigned negative charge : -517.6097 centred at (gu) : 83.04806 84.28088 84.96863 start vw surface at 0.1100000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 89533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29575 grid for indexing accessible points = 1.400000 m= 32565 mr = 62453 m= 4514 mr = 23781 m= 218 mr = 2624 m= 3 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 687 time to turn everything in is 0.4600000 number of dielectric boundary points 37918 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 271 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 25641 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) : 0.6012904 object centre at (A) : 21.58400 42.97300 41.97350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8809719E-03 -1.6926760E-02 midg,1,midg; midg,igrid,midg -1.2148395E-02 -2.1136135E-02 1,midg,midg; igrid,midg,midg -6.7762225E-03 -1.1454628E-02 gauss-seidel spectral radius is 0.9985490 estimated iterations to convergence 208 setup time was (sec) 0.6900000 now iterating at: 17:44:44 rms-change max change #iterations 4.426656 173.9350 at 10iterations 2.015684 62.26271 at 20iterations 0.9219430 28.32650 at 30iterations 0.4230928 13.11851 at 40iterations 0.1937469 6.268673 at 50iterations 8.8608995E-02 2.825897 at 60iterations 4.0611751E-02 1.188992 at 70iterations 1.8564660E-02 0.5508342 at 80iterations 8.5472129E-03 0.2614245 at 90iterations 3.9216541E-03 0.1192775 at 100iterations 1.8001993E-03 5.6540489E-02 at 110iterations 8.3652436E-04 2.3928642E-02 at 120iterations finished qdiffx linear iterations at : 17:44:52 total time elapsed so far: 8.400000 # loops : 120 mean,max change (kT/e) : 8.3652436E-04 2.3928642E-02 energy calculations done at 8.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.530000 DelPhi exited at 17:44:52 8.535u 0.219s 0:09.03 96.7% 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 17:44:52 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 = 3421 !!! WARNING: GLN 381 has a net charge of -0.2720 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: 2.705807 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): -8.019000 51.18700 ymin,ymax (A): 15.35100 70.59500 zmin,zma (A): 12.96400 70.98300 x,y,z range (A): 59.20600 55.24400 58.01900 scale (grids/A): 2.705807 object centre (A): 21.58400 42.97300 41.97350 number of atom coordinates read : 3421 total number of charged atoms : 3275 net assigned charge : -5.771983 assigned positive charge : 511.8365 centred at (gu) : 79.74530 81.35551 82.49303 assigned negative charge : -517.6097 centred at (gu) : 79.57193 81.42108 82.45284 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 207208 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29575 grid for indexing accessible points = 1.400000 m= 106305 mr = 151432 m= 36715 mr = 86809 m= 7797 mr = 29084 m= 941 mr = 5599 m= 39 mr = 573 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 2496 time to turn everything in is 1.160000 number of dielectric boundary points 85499 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 26198 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) : 1.803871 object centre at (A) : 21.58400 42.97300 41.97350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1767836 -0.2791750 midg,1,midg; midg,igrid,midg -3.9592288E-02 -0.2046534 1,midg,midg; igrid,midg,midg -0.3754607 -0.1766077 gauss-seidel spectral radius is 0.9992529 estimated iterations to convergence 289 setup time was (sec) 1.420000 now iterating at: 17:44:54 rms-change max change #iterations 10.81809 358.9547 at 10iterations 6.349343 146.6866 at 20iterations 3.701035 67.26398 at 30iterations 2.151861 42.30731 at 40iterations 1.245392 24.26433 at 50iterations 0.7187527 14.90643 at 60iterations 0.4142462 6.919896 at 70iterations 0.2385726 3.951845 at 80iterations 0.1372108 2.398754 at 90iterations 7.8853905E-02 1.442188 at 100iterations 4.5331575E-02 0.7230911 at 110iterations 2.6074793E-02 0.4607010 at 120iterations 1.4991702E-02 0.2443666 at 130iterations 8.6180288E-03 0.1464481 at 140iterations 4.9686022E-03 8.3840847E-02 at 150iterations 2.8650889E-03 4.9335480E-02 at 160iterations 1.6718264E-03 2.9981613E-02 at 170iterations 9.8641485E-04 1.8728256E-02 at 180iterations finished qdiffx linear iterations at : 17:45:07 total time elapsed so far: 14.05000 # loops : 180 mean,max change (kT/e) : 9.8641485E-04 1.8728256E-02 energy calculations done at 14.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.19000 DelPhi exited at 17:45:07 14.190u 0.242s 0:14.72 98.0% 0+0k 0+0io 0pf+0w