Sun Oct 9 12:48:25 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 Sun Oct 9 2011 at 12:48:25 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6990260 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): -6.657000 44.27100 ymin,ymax (A): -14.06500 36.16900 zmin,zma (A): 2.277000 44.74500 x,y,z range (A): 50.92800 50.23400 42.46800 scale (grids/A): 0.6990260 object centre (A): 18.80700 11.05200 23.51100 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500013 assigned positive charge : 363.5891 centred at (gu) : 89.57700 91.31518 90.62432 assigned negative charge : -360.0895 centred at (gu) : 89.60844 91.48428 90.66962 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7826 nv = 96 ne = 84 npr = 47599 no. pairs analyzed = 47599 no. exposed pairs = 3028 no. arc points = 20781 no. surface atoms = 1022 nbur = 1344 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 517 mr = 4343 m= 3 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3910 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2011 ## 216 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8828 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.1315719E-08 4.3467732E-09 midg,1,midg; midg,igrid,midg 7.9992887E-08 -7.3125783E-08 1,midg,midg; igrid,midg,midg 4.3643769E-08 9.8371249E-09 gauss-seidel spectral radius is 0.9893644 estimated iterations to convergence 79 setup time was (sec) 0.3800000 now iterating at: 12:48:26 rms-change max change #iterations 0.2052887 29.27154 at 10iterations 2.5042679E-02 3.564306 at 20iterations 3.4964778E-03 0.4684067 at 30iterations 7.1531575E-04 0.1057396 at 40iterations 2.1735555E-04 3.1211853E-02 at 50iterations finished qdiffx linear iterations at : 12:48:29 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 2.1735555E-04 3.1211853E-02 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 12:48:29 3.369u 0.167s 0:03.85 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 Sun Oct 9 2011 at 12:48:29 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.097078 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): -6.657000 44.27100 ymin,ymax (A): -14.06500 36.16900 zmin,zma (A): 2.277000 44.74500 x,y,z range (A): 50.92800 50.23400 42.46800 scale (grids/A): 2.097078 object centre (A): 18.80700 11.05200 23.51100 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500013 assigned positive charge : 363.5891 centred at (gu) : 88.73052 93.94505 91.87257 assigned negative charge : -360.0895 centred at (gu) : 88.82487 94.45251 92.00859 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82355 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20781 grid for indexing accessible points = 1.400000 m= 32275 mr = 57160 m= 6018 mr = 23925 m= 612 mr = 3925 m= 18 mr = 312 m= 0 mr = 4 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 35952 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 114 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17673 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) : 0.6990260 object centre at (A) : 18.80700 11.05200 23.51100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3381216E-02 9.0429001E-03 midg,1,midg; midg,igrid,midg 1.6883684E-02 -4.6438277E-02 1,midg,midg; igrid,midg,midg 5.9108432E-02 -1.6531443E-02 gauss-seidel spectral radius is 0.9988411 estimated iterations to convergence 233 setup time was (sec) 0.6300000 now iterating at: 12:48:30 rms-change max change #iterations 4.916265 201.0506 at 10iterations 2.441823 88.04705 at 20iterations 1.211652 39.36993 at 30iterations 0.6020533 19.71292 at 40iterations 0.2989611 9.926394 at 50iterations 0.1491962 4.188519 at 60iterations 7.4343830E-02 2.014000 at 70iterations 3.7116412E-02 1.106667 at 80iterations 1.8633159E-02 0.5365410 at 90iterations 9.4360523E-03 0.2670746 at 100iterations 4.8572691E-03 0.1400471 at 110iterations 2.5844318E-03 8.4091187E-02 at 120iterations finished qdiffx linear iterations at : 12:48:37 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 2.5844318E-03 8.4091187E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 12:48:38 7.880u 0.212s 0:08.35 96.8% 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 Sun Oct 9 2011 at 12:48:38 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.145617 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): -6.657000 44.27100 ymin,ymax (A): -14.06500 36.16900 zmin,zma (A): 2.277000 44.74500 x,y,z range (A): 50.92800 50.23400 42.46800 scale (grids/A): 3.145617 object centre (A): 18.80700 11.05200 23.51100 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500013 assigned positive charge : 363.5891 centred at (gu) : 88.09563 95.91755 92.80874 assigned negative charge : -360.0895 centred at (gu) : 88.23723 96.67876 93.01277 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 190015 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20781 grid for indexing accessible points = 1.400000 m= 100668 mr = 138063 m= 40185 mr = 82549 m= 11233 mr = 32526 m= 2272 mr = 8520 m= 310 mr = 1650 m= 13 mr = 221 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 81167 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 17796 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) : 2.097078 object centre at (A) : 18.80700 11.05200 23.51100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5038595 -3.8310008E-03 midg,1,midg; midg,igrid,midg 0.2974317 -0.4602582 1,midg,midg; igrid,midg,midg 0.6203983 -0.4578350 gauss-seidel spectral radius is 0.9993029 estimated iterations to convergence 299 setup time was (sec) 1.520000 now iterating at: 12:48:39 rms-change max change #iterations 11.06927 449.6385 at 10iterations 6.573807 142.9756 at 20iterations 3.892495 74.06637 at 30iterations 2.305732 41.41838 at 40iterations 1.362419 24.52394 at 50iterations 0.8047358 14.05520 at 60iterations 0.4739183 7.920090 at 70iterations 0.2787026 4.986656 at 80iterations 0.1637381 2.858072 at 90iterations 9.6149698E-02 1.605200 at 100iterations 5.6581758E-02 0.9717865 at 110iterations 3.3295766E-02 0.6250572 at 120iterations 1.9736189E-02 0.3375683 at 130iterations 1.1830536E-02 0.2127628 at 140iterations 7.2202208E-03 0.1337662 at 150iterations 4.5649866E-03 8.9622498E-02 at 160iterations 3.0319178E-03 6.4781189E-02 at 170iterations 2.1525798E-03 4.5703888E-02 at 180iterations finished qdiffx linear iterations at : 12:48:51 total time elapsed so far: 12.94000 # loops : 180 mean,max change (kT/e) : 2.1525798E-03 4.5703888E-02 energy calculations done at 12.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 12:48:51 13.064u 0.218s 0:13.56 97.8% 0+0k 0+0io 0pf+0w