Re: [AMBER] Ca ion bond distances restraints with chelator ?

From: David A Case <>
Date: Thu, 25 Oct 2018 10:26:03 -0400

On Thu, Oct 25, 2018, Michael Shokhen wrote:

> # makeDIST_RST
> Currently configured for up to 50000 atoms
> Using MAP file /var/spool/scratch/shokhen/amber16/dat/map.DG-AMBER
> ERROR no map function for CA CA :data= 349 CA CA 1 MOL O1 2.4

By default, atoms are not mapped to "themselves" by makeDIST_RST: you
have to include a specific mapping if you want that behavior.
(Historical note: the original motivation was to catch typos when large
numbers of restraints derived from NMR data were being processed.)

> Indeed the map.DG-AMBER file does not contain Ca parameters,
> But it contains data for ZN. I tried to add the data for CA by analogy.
> Nevertheless AMBER reported error message again.

It's hard to know whether what you did "by analogy" was correct or not,
since you didn't report the exact changes. It should be something like


However, if you have just a few restraints, writing out the &rst namelists
by hand is often easier than using makeDIST_RST. The latter was
designed for NMR studies where (a) there are a large number of
restraints, and (b) "7-column" files are being written by other parts of
the spectrum analysis pipeline.

...good luck...dac

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Received on Thu Oct 25 2018 - 07:30:04 PDT
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