AMBER Archive (2007)

Subject: AMBER: Question

From: dykyy (alex.dikiy_at_biotech.ntnu.no)
Date: Tue Nov 06 2007 - 07:12:46 CST


(subscribe amber)

Hi,
I have some questions concerning running of AMBER 9.

I will be very grateful to you if you can explain me how to resolve our
problems we have related to AMBER 9.0.

We are working with a Zn-containing enzyme (MsrB family).
Using CYANA software we calculated the structure of the protein.
Now we would like to energy minimize the structure using AMBER 9.0.

I started with tleap program and everything went well till reading of
pdb file.
Amber found problems with N-terminal amidic proton and Zn atom.
Herewith attached please find an error messages provided by AMBER
(tLEaP_output.txt) and our PDB fie (totsed.txt) we are using.

1. NH of Met-1. It says that amidic proton does not exist for Met1, even
if it is termed in analogy to all others amidic protons. May be, since
it is N-terminal residue, I should add coordinates of two other amidic
protons? How I can get those coordinates? I have nevertheless feeling,
that this is fine and I can continue to work even with this message. Is
it correct?

2. My previous experience with minimization of metaloproteins using,
probably Amber 6, was that we simply added the metal ion as a last
residue (in that case it was a Cu2+ ion). I tried to do the same hear.
However, it apparently does not work. May be Zn2+ ion is not included in
the AMBER9 data base? If so, could you please advise me how to include
it, in which file, etc.
Could you please let me know how to overcome this difficulty.

Another question. How should I say to AMBER about distances between Zn
ion and coordinating it cysteines. Just, in AMBER upl file, create 4-8
constraints about distances between Zn and Sg atoms and angles in
analogy with normal distance constraints?

I thank you in advance for your assistance.
Best, Alex Dikiy.

Majordomo_at_scripps.edu wrote:

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-- 
Alexander Dikiy
Associate Professor,
Department of Biotechnology, 
Faculty of Natural Sciences and Technology,
Norwegian University of Science and Technology,
Trondheim, NO-7491 
Norway

e-mail: Alex.dikiy_at_biotech.ntnu.no Phone: +47-73597863 Fax: +47-73591283

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