AMBER Archive (2009)

Subject: Re: [AMBER] restraining atoms

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Jan 22 2009 - 08:55:35 CST

the A/B etc is not retained in leap. all residues are numbered sequentially.

On Thu, Jan 22, 2009 at 9:53 AM, neville forlemu
<neville_forlemu_at_yahoo.com> wrote:
>
> I have a quick question about restraining atoms, during a minimization or md run using amber.
> Lets say you have a homotetramer (subunits A,B,C,D).
> In the pdb file each subunit the residues are number as follows
> A1-A300, B1-B300 etc
>
> During
> a minimization, where I intend to only minimize the salts and water can
> I restrain all the residues in the protein by specifying
>
> res 1 1200
>
> or should I differentiate the subunits like
>
> res A1-A300 etc.
>
> Thanks
> Neville
>
> --- On Thu, 1/22/09, Lake, Thomas <thomas.lake08_at_imperial.ac.uk> wrote:
> From: Lake, Thomas <thomas.lake08_at_imperial.ac.uk>
> Subject: [AMBER] (no subject)
> To: amber_at_ambermd.org
> Date: Thursday, January 22, 2009, 7:43 AM
>
> I am trying to generate an average PDB structure, from a PDB containing
> multiple structures. I think I need to use ptraj to do this, but am not
> sure what to write in the input file. Can anyone help.
>
> Thanks
>
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