[gmx-users] Regarding terminal residue parameters (Capping)

[Harry Mark Greenblatt]

BS”D



I am trying to simulate a multichain amino acid structure. PDB ID 2BEG.

I am experiencing problems with the C and N terminal residues i. e. C-ALA
and N-LEU.

An abnormal non-bonded interaction keeps forming between atoms C from ALA42
and N from LEU17.

Do you mean from Ala42 of Chain A to Leu17 of Chain B?

If the chain specifiers are intact in the pdb input file then no bond should be formed.  What does the  output of pdb2gmx say?

Harry

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Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology           harry.greenblatt at weizmann.ac.il<../../owa/redir.aspx?C=QQgUExlE8Ueu2zs5OGxuL5gubHf97c8IyXxHOfOIqyzCgIQtXppXx1YBYaN5yrHbaDn2xAb8moU.&URL=mailto%3aharry.greenblatt%40weizmann.ac.il>
Weizmann Institute of Science        Phone:  972-8-934-6340
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