You can also run leap with your normal 1-149 no capping groups, save the pdb
file and in the new pdb rename H2 of res 1 to C of ACE and OXT of 149 to N
of NME.
Once leap runs correctly and you can visualize your molecule in VMD or
similar, then start worrying about running sander.
Melinda
On 6/25/07, priya priya <priyaanand_27.yahoo.co.in> wrote:
>
> you can use xleap to add ACE and NME to cap the system
>
> *backy <backy.ibms.sinica.edu.tw>* wrote:
>
> Actually, how users cap the protein terminal?
> For example, by which kind of program to put the initial coordinates for
> ACE
> and NME groups?
>
> backy
> ----- Original Message -----
> From: "David A. Case"
> To:
> Sent: Thursday, June 21, 2007 1:10 PM
> Subject: Re: AMBER: problems in adding ACE and NME group
>
>
> > On Thu, Jun 21, 2007, backy wrote:
> >
> >> If there is a need in placing the whole ACE and NME group, how should I
> >> input their initial coordinations?
> >
> > This is a very rare thing to do, and Amber admitedly doesn't make it
> very
> > easy. It isn't something I would recommend just "for practice".
> >
> > You might use a homology-modeling program to add alanine at both ends,
> > then
> > delete the atoms you don't need, and change the residue names to ACE and
> > NME.
> >
> > ....dac
> >
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> >
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Received on Wed Jun 27 2007 - 06:07:41 PDT
