AMBER Archive (2009)

Subject: Re: [AMBER] ptraj image

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Wed Dec 09 2009 - 07:41:54 CST

> I have a system which has two antiparallel monomers. I m using the following
> commands below using Amber 9. I can get the correct distances between Ca-Ca
> but the values get messed up with helix.rmsd and equil.rmsd after 90 ns. Any
> suggestions?

It is unclear what "messed up" means. If the RMSd is jumping to large
values (~box size) then it is likely an imaging issue. This wouldn't be
seen with the distance command since it images by default (unless the
"noimage" keyword is specified).

> trajin prod197.mdcrd.gz 1 50 1
>
> center :1-144 origin mass
> image origin center

try:

center :54-71 mass origin
image origin
center :54-71,126-143 mass origin
image origin center familiar

[Otherwise, we need more details to decipher...]

-- tec3

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