I have PDB structure of RNA molecule. in that adenine, guanine, cytosine
and uracil are named as ADE, GUA, CYT and URI respectively. while loading
it in xleap i got the message "unknown residues:" and "created a new atom
named: O2 within residues: ... etc".
then i viewed my molecule in xleap i found it was completely distorted and
all connections between the molecules were disconnected. and It looks
totally different from the actual PDB structure.
On Sat, Mar 5, 2016 at 12:44 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Sat, Mar 5, 2016 at 2:04 AM, Sreemol G <sreemolinfo.gmail.com> wrote:
>
> > Hello all,
> >
> > Can anyone please tell me how adenine, thymine, cytosine, Guanine and
> > uracil are defined in leap??
> >
>
> The normal way?
>
> Do you have a more specific question? You can use the "edit" command in
> xleap to investigate individual residues after you load a force field. For
> example, inside xleap:
>
> source leaprc.ff14SB
> edit A
>
> That will show you adenine
>
> edit DA
>
> That will show you deoxyadenine.
>
> (These residues are actually defined in the residue template libraries that
> are loaded as part of a force field, not actually by leap itself). But I
> can't expect to give information useful to you unless you provide a more
> concrete description of what it is you are trying (but unable) to do.
>
> HTH,
> Jason
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>
--
With kind regards,
G. Sreemol
M.Tech (Computational Biology)
Anna university
Chennai.
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Received on Fri Mar 04 2016 - 23:30:10 PST
