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AMBER Archive (2009)Subject: RE: [AMBER] Principle Questions
From: Ross Walker (ross_at_rosswalker.co.uk)
Hi Bill,
> I have some principle questions about AMBER.
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
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
No you cannot use NME at both ends because this would not make sense. In the case of the dye you have:
O
In your proposal if you used NME for the dye end of the linker you would have:
H H
which does not make chemical sense...
> 4- If my protien pdb
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
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