Re: AMBER: neutral terminals

From: Carlos Simmerling <>
Date: Thu, 2 Aug 2007 08:04:15 -0400

I think that unless you add restraints to the cut ends they are likely
to move since they no longer have any of the interactions from before.
You could try and see, perhaps with just minimization they won't move
much (but certainly dynamics would not be possible).
I think you will just have to try and see. For pure Amber runs you could
leave them uncapped (and uncharged) by turning off residue name
mapping so that they won't get converted to the N/C terminal residues.
If Gaussian needs the real caps, then it can be hard to add them unless
you save some atoms from the previous residues and allow leap to use them
for building the caps. even then you need to minimize the added groups while
restraining what you had before, and then min the whole thing.
It's not very automatic in Amber, perhaps people know of other programs that
will facilitate this.

On 8/1/07, Jena M <> wrote:
> Hi,
> I cut residues of a protein to create a sphere of 25 A around a ligand and I
> want to minimise it. I need the C- and N-terminals of the fragments in the
> sphere to be neutral as the minimised structure is to be used as input for
> Gaussian. According to some posts in the amber list the way to do this is to
> use protecting groups.
> As the sphere has about 20 peptide fragments I need to introduce a high
> number of protecting groups. My question is: Does this can introduce some
> type of artefact in the system, such as, a change in the conformation of
> neighbouring residues of the capping groups? Is there another way to make
> the neutral terminals?
> Thanks
> Jena
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Received on Sun Aug 05 2007 - 06:07:25 PDT
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