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

Harry Mark Greenblatt harry.greenblatt at weizmann.ac.il
Mon Jul 10 15:21:35 CEST 2017


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 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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