AMBER Archive (2008)

Subject: Re: AMBER: impropers over bonds between sidechains

From: M. L. Dodson (activesitedynamics_at_comcast.net)
Date: Thu Aug 14 2008 - 21:29:54 CDT

On Fri, Aug 15, 2008 at 10:42:05AM +0930, Grange Hermitage wrote:
> 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.

How about just deleting the ones that are immaterial?

Bud Dodson 

-- 
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email:	mldodson-at-comcast-dot-net
Phone:	eight_three_two-56_three-386_one
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