AMBER Archive (2009)

Subject: [AMBER] Principle Questions

Date: Tue Jul 07 2009 - 02:50:53 CDT

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?
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?
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
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?
Thanks in Advance
S. Bill

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