AMBER Archive (2005)

Subject: RE: AMBER: new residue

From: Douali, Latifa (latifa.douali_at_pnl.gov)
Date: Wed Jul 27 2005 - 11:09:01 CDT

Hi

Thank you Kristina for your reply.
I already identified the haed and the tail of my residue and set up the
frcmod file.
The pdb file of the polymer looks fine when I load it in VMD.
I expect my monomer structure (into the polymer) to be planar. In Xleap,
the residue is palanar when I load it as a monomer but it is not the
case within a polymer. I have to mention here that my polymer pdb file
is created by another program. Is there a mismatch between the Xleap and
the other softwares? Thanks

Latifa

> Just a guess, but you might make sure your head and tail atoms are
identified correctly so the proper connections are made. Probably need
to give more
> info on what weird means...

G'luck,
Kristina

Quoting "Douali, Latifa" <latifa.douali_at_pnl.gov>:

> Dear amber users,
>
>
> I have created a new nucleic acid residue. When I edit my new monomer
> residue in xleap it looks fine. When I try to insert it into a
> polymer, I obtain a weird structure. (I load the polymer by loadpdb
> command in
> Xleap)
> How can I make nucgen recognise my new residue?
>
> Thank you very much
>
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