RE: [AMBER] Principle Questions

From: Ross Walker <>
Date: Wed, 8 Jul 2009 00:42:42 +0100

Hi Bill,

> I have some principle questions about AMBER.
> 1- In one step, we neutralize our proteins with adding ions using
> Addions command, what is the origin of this negative charge, and why
> this negative not neutralized during adding H atoms?

Not all amino acids are neutral and in reality their charge / protonation state is a function of pH. For example histidine can be double protonated (HIP) = +1 charge. Aspartate and glutamate are typically deprotonated at physiological pH (and in AMBER) and thus have -1 charges.

> 2- I asked one question before about missing a part of my PDB file, my
> protein is 770 residue, the residues between 340 to 375 are missing.
> This area is so far from my active site. So, what should I do, go on
> without paying any attention to these missing residues, or, build it
> (and how), or add TER card between residue 339 and 376?

This is a tough one. It would come down to how critical those residues are. Can one remove them in experiment and the enzyme is still active / doesn't fall apart? If the answer is no then you need them in your simulation as well. Your best bet, if you know the sequence, is to take a look at some homology modelling / structure prediction codes and see if you can model in the missing residues.

> 3- In tutorial A1, can we use NME for capping the dye and linker? in
> the tutorial he used NME for capping the dye and used ACE for
> capping dye-end
> linker.

No you cannot use NME at both ends because this would not make sense. In the case of the dye you have:


In your proposal if you used NME for the dye end of the linker you would have:

      H H
    H H

which does not make chemical sense...

> 4- If my protien pdb
> file has crystallic water molecules and I added explicit water
> molecules using solvateoct TIP3PBOX command, in this case, my
> crystallographic water molecules will be treated as TIP3PBOX molecules,
> isn't it?

Yes and in reality this is correct since the waters are degenerate. I.e. in experiment if you were to somehow deuterate the 'crystallographic' waters and then dissolve your crystal in bulk water and then recrystalize it would you still get deuterated waters for your crystal waters? I believe not hence it makes perfect sense to consider them to be bulk water which is what leap should do.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Tue Jul 07 2009 - 18:10:20 PDT
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