Re: [AMBER] Distance based mask and reference

From: David Case <>
Date: Sat, 20 May 2017 07:19:52 -0600

On Fri, May 19, 2017, Marion, Antoine wrote:
> I guess that there is a problem in the behavior of the "-ref" command
> line option in sander (AmberTools15-17).
> "refc input (optional) reference coords for position restraints; also
> used for targeted MD"
> What I understand from this is that the coordinates present in "refc"
> should be used to set an atom mask when "ntr > 1".

The piece of the manual you cite was written (long) before we implemented
anything like distance-based masks. But it looks like the correct thing
to do is to update the code in the manner you suggest, since atommasks can now
depend upon the values in the coordinates, and not just on atom numbers/names.

> I would for example expect "bellymask" to work on reference coordinates
> instead of input ones, but "refc" is not read when "ibelly = 1".

This is a slightly bigger fix, but should still be do-able.
> I fixed that locally to get the behavior that I expect, but I might
> be missing some more global vision of the code to be sure that it is
> correct.

If you are willing/able to send some proposed patch files, that would be

Thanks for the report....dac

AMBER mailing list
Received on Sat May 20 2017 - 06:30:02 PDT
Custom Search