From: yxiong_at_mail.ccnu.edu.cn
Date: Thu Nov 27 2003 - 06:57:35 CST
I think it should due to HIS residue which may be HSD, HSE or HSP.
Please see NAMD TUTORIAL:
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¡±).
>From: Hua Wong <wong_at_ebgm.jussieu.fr>
>Reply-To:
>To: namd-l_at_ks.uiuc.edu
>Subject: namd-l: problems with psfgen
>
>I need some help about psfgen.
> Does HIS residues cause problems for psfgen?
> Is it due to the PDB file format used?
> What are the possible cause for this error?
>
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> unknown residue type HIS
> extracted 336 residues from pdb file
> Info: generating structure...
> unknown residue type HIS
> ERROR: failed on end of segment
>
>
>
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