AMBER Archive (2004)

Subject: Re: AMBER: How to add ACE and NME groups?

From: Ben Cossins (bcc_at_soton.ac.uk)
Date: Tue Feb 24 2004 - 10:47:43 CST

Hi Malgorzata,
  I have added protecting groups to the ends of my proteins by manually
editing the pdb input file. xleap will add these groups for you but it will
not place them.

you can add an NME residue by manually adding a NME N atom to the end of your
protein in your pdb file. xleap will add the rest of the NME for you.
However you must place the N atom yourself. This can be done by either
working out the vector of the previous backbone bond and adding your N at the
point of the same vector added on to the end of the protein, or you can just
try it manually. in both cases when you have loaded the pdb file into xleap
it is a good idea to use the relaxing algorithum to give the NME residue a
better position.

Subsiquent minimisation should iron out the poor position of the NME.

I have not tried this with a NHE atom. However when i added a ACE protective
group I added a C atom not a N. As this would make sense.

This is not a perfect way of going about this problem but it is the best I
could find using xleap.

Ben Cossins

On Monday 23 Feb 2004 9:47 am, Małgorzata Jarończyk wrote:
> I work with protein model without loops and terminals and I want to add
> protecting groups to head and tail of the helices. How can I do this in the
> Xleap program? What is the difference between the two protecting groups NMe
> and NHE? Can you help me?
>
> Malgorzata Jaronczyk

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