Re: [AMBER] restraining many individual atoms

From: James Kress <>
Date: Mon, 20 Apr 2020 15:37:44 -0400

Is there no way you can renumber the atoms to facilitate grouping?

James Kress Ph.D., President
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-----Original Message-----
From: Ignacio General <>
Sent: Monday, April 20, 2020 2:06 PM
Subject: [AMBER] restraining many individual atoms

 Dear Amber users,

I need to do some MD runs with pmemd.cuda, restraining the position of
several hundred atoms. The problem is that they are not sequential, so that
I can't use ranges of values, but have to list them individually. ntr=1 with
restraintmask only allows 256 characters, so this is not good enough.
I thought of using the old group specification but, again, since the atoms
are not ordered, I need to create a group for each atom. In that case, I
will need to have a sequence of several hundred groups, something like this:
Group 1:
ATOM 265
Group 2:
ATOM 267
Group 200:
ATOM 5215

Anybody can think of a better way of doing this? And if I do it this way, is
there a limit to the number of groups that can be given to pmemd.cuda?

Thanks for your help,

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Received on Mon Apr 20 2020 - 13:00:02 PDT
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