Re: [AMBER] Distance based mask and reference

From: Marion, Antoine <>
Date: Sat, 20 May 2017 13:44:48 +0000

Thank you very much for your answer.
I would be glad to send you a patch.

I will juste make some more tests and I will send it to you very soon.

Best regards,

> Le 20 mai 2017 à 15:20, David Case <> a écrit :
>> 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
> great.
> Thanks for the report....dac
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Received on Sat May 20 2017 - 07:00:03 PDT
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