AMBER Archive (2007)

Subject: Re: AMBER: tgtrmsmask and tgtfitmask

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Jul 10 2007 - 06:26:08 CDT

yes, they are switched in the amber9 manual.
fitmask is for the atoms to use for the best-fit,
rmsmask is the atoms for the actual rmsd calculation.

On 7/9/07, Holly Freedman <freedman_at_phys.ualberta.ca> wrote:
> Dear AMBER support,
>
> I believe that there is a mistake in the AMBER 8 and 9 manuals when describing tgtrmsmask and
> tgtfitmask, the definitions seem to be reversed. This is my impression from reading posts by Viktor
> Hornak on the AMBER reflector and also from my recent experience trying the TMD option. Am I right
> about this?
>
> Thanks,
> Holly
>
>
> --
> Department of Physics, University of Alberta
> Edmonton CANADA
>
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