From: yxiong_at_mail.ccnu.edu.cn
Date: Fri Nov 28 2003 - 04:02:05 CST
Dear sir,
In the tutorial of NAMD program, there is the following advice:
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Histidine Residues. Of the 20 amino acids, histidine is the only
one which ionizes within the physiological pH range ( ˘ 7.4). This
effect is characterized by the pKa of the amino acid side chain. For
histidine, the value is 6.04. This leads to the possiblilty of different
protonation states for histidine residues in a protein, and makes the
consideration of the proper state important in MD simulations. The
viable states are one in which the nitrogen of histidine is protonated
(listed with residue name ¡°HSD¡± in the topology file), one in which
the nitrogen of histidine is protonated (¡°HSE¡±), and one in which
both nitrogens are protonated (¡°HSP¡±).
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Since the H atoms are not available from the original pdb file, how can I know
which type HIS belong to?
Thanks!
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