AMBER Archive (2009)

Subject: Re: [AMBER] Acetylate and Amidate

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Jul 09 2009 - 06:52:28 CDT

it really depends a lot on what you have in the pdb. is it only coordinates
of the part you will simulate, or is it the full protein and you will
simulate just part of the pdb? if the latter, then keep the residue before
and after and change the residue names to ACE and NH2, delete the atoms that
don't exist on those capping groups. it's hard to be more specific without
knowing exactly what you are doing.

On Wed, Jul 8, 2009 at 6:47 PM, Alison Saunders <alison.m.saunders_at_gmail.com
> wrote:

> What command in xleap do I use to add the ACE and the NH2 to the beginning
> and end of my pdb file protein?
>
> On Wed, Jul 8, 2009 at 3:22 PM, Carlos Simmerling <
> carlos.simmerling_at_gmail.com> wrote:
>
> > add ACE and NH2 to your sequence
> >
> >
> > On Wed, Jul 8, 2009 at 6:19 PM, Alison Saunders <
> > alison.m.saunders_at_gmail.com
> > > wrote:
> >
> > > I need to acetylate (Ac) and amidate (NH_2) the N- and C- termini of a
> > > protein fragment, to emulate the fragment as a native protein. Does
> > anyone
> > > know how this can be done using the existing residues on xleap?
> > >
> > > Thanks,
> > > Alison Saunders
> > > UC Davis Physics REU Program Member
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