Re: [AMBER] Restraint file for amber20 with pmemd.cuda implementation

From: David A Case <>
Date: Tue, 25 Jan 2022 13:11:24 -0500

On Tue, Jan 25, 2022, Prithviraj Nandigrami wrote:

>Here is the input file:
>simann with pos-restraint on receptor + dist restraint on ligand
> &cntrl
> ntr = 1,
> &wt type='END', /

You are setting ntr=1, but not setting restraintmask and restraint_wt.
This makes the program think you are using the "old" GROUP identification
cards, But there aren't any of those in your input file -- they should come
after the file redirection cards. (It's not clear to me how this input could
have worked in Amber12.)

It's easiest to set restraintmask and restraint_wt in the cntrl namelist.
Or you can use the group input, as described in Section 23.3. Section 21.5
describes the sections of the input file, and what they need to contain.

....good luck....dac

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Received on Tue Jan 25 2022 - 10:30:02 PST
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