AMBER Archive (2008)

Subject: Re: AMBER: peptide MD

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Oct 27 2008 - 13:07:11 CDT

you might want to do this using GB to start, and then 1 or more
distance restraints to pull them close enough that you can convert the
restart file to a pdb, then load back into leap and solvate them.
you'll need to decide on the box size that you want (the
concentration), and that will determine how close you pull them
together.

On Mon, Oct 27, 2008 at 1:52 PM, Gustavo Seabra
<gustavo.seabra_at_gmail.com> wrote:
> On Mon, Oct 27, 2008 at 1:47 PM, Beale, John wrote:
>
>> One PDB file for each.
>
> OK, then I suppose you should start by creating a PDB file with your
> "system" (the 2 peptides) in some suitable orientation. Make sure
> there is a "TER" card between the two. The you can just load that into
> leap as you would with any other PDB file.
>
> Gustavo.
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