I'm using ptraj because ambpdb fail for big systems, but i try your
method. Anyway, can i solve it with ptraj?
Thanks
El jue, 07-01-2010 a las 09:35 -0500, Jason Swails escribió:
> You are trying to create a pdb using ambpdb? If this is the case,
> then these atom number/residue number limits are hard-coded into
> ambpdb in the source code. If you want to add another order of
> magnitude to the available residue number and atom number, you'll have
> to change the Formats in $AMBERHOME/src/etc/ambpdb.f and recompile it.
>
> In my version of ambpdb.f, these format statements are located around
> line 790. (I believe you'll want to change I5 into I6 for atom numbers
> and I4 into I5 for residue numbers, though I'm not comfortable enough
> with fortran format statements to know if these changes alone will be
> enough to accomplish what you're trying to).
>
> Good luck!
> Jason
>
> 2010/1/7 Fernando Martín García <fmgarcia.cbm.uam.es>:
> > Hello:
> >
> > I have problem with the identification number of residue and atom. The
> > problem is that when residue is over 9999, the numeration change to
> > ****. The problem is the same in atom number.
> >
> > I installed amber10 but i obtain the same result that in amber8. Can
> > anybody help me to know if there is an option to modify the numeration?
> >
> > This is my result for residues
> >
> >
> > ATOM 42297 H1 WAT 9998 137.785 -11.529 53.410 0.00 0.00
> > ATOM 42298 H2 WAT 9998 137.132 -12.797 53.917 0.00 0.00
> > ATOM 42299 O WAT 9999 103.772 58.806 9.424 0.00 0.00
> > ATOM 42300 H1 WAT 9999 104.549 59.165 9.852 0.00 0.00
> > ATOM 42301 H2 WAT 9999 103.107 58.786 10.113 0.00 0.00
> > ATOM 42302 O WAT **** 82.586 -43.191 45.785 0.00 0.00
> > ATOM 42303 H1 WAT **** 82.673 -42.371 46.270 0.00 0.00
> > ATOM 42304 H2 WAT **** 82.388 -42.919 44.889 0.00 0.00
> > ATOM 42305 O WAT **** 101.964 50.272 72.323 0.00 0.00
> >
> > and for atoms:
> >
> > ATOM 99996 H1 WAT **** 91.672 34.379 287.571 0.00 0.00
> > ATOM 99997 H2 WAT **** 91.016 35.674 287.141 0.00 0.00
> > ATOM 99998 O WAT **** -51.910 -10.370 11.200 0.00 0.00
> > ATOM 99999 H1 WAT **** -51.086 -9.922 11.394 0.00 0.00
> > ATOM ***** H2 WAT **** -52.292 -10.552 12.059 0.00 0.00
> > ATOM ***** O WAT **** 16.143 -15.117 11.351 0.00 0.00
> > ATOM ***** H1 WAT **** 15.335 -15.359 11.803 0.00 0.00
> > ATOM ***** H2 WAT **** 16.467 -14.355 11.832 0.00 0.00
> >
> >
> > Thank you
> > --
> > Fernando Martín García.
> > Centro de Biología Molecular "Severo Ochoa".
> > C/ Nicolás Cabrera, 1.
> > Campus UAM. Cantoblanco, 28049 Madrid. Spain.
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
--
Fernando Martín García.
Centro de Biología Molecular "Severo Ochoa".
C/ Nicolás Cabrera, 1.
Campus UAM. Cantoblanco, 28049 Madrid. Spain.
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Received on Thu Jan 07 2010 - 07:30:03 PST
