AMBER Archive (2008)

Subject: AMBER: impropers over bonds between sidechains

From: Grange Hermitage (ghermitage_at_gmail.com)
Date: Thu Aug 14 2008 - 20:12:05 CDT

Hi,

I have caps on sidechains to handle a bond being formed between a LYS and
ASP derivative new residues.
These new residues are charge fitted by RESP on Gaussian output.
When prepgen generates a prepin file for each of these new residues,
impropers are generated for what will be the amide bond between the LYS and
ASP derivative residues. However, the atoms of the sidechain caps will be
removed and impropers referring to the removed atoms presumably lost. How to
specify an improper that refers to atoms of two residues? (the residues are
not adjacent in the sequence).

I see in a send some years ago that impropers in a prepin are ignored by
leap.
Is this still the case?
If so, the problem of how to specify in prepin an improper over atoms of two
sidegroups is immaterial.

cheers,
    John.

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