Re: [AMBER] imin=5 not working in AMBER16?

From: Paul Mortenson <>
Date: Mon, 4 Dec 2017 14:04:04 +0000

Dear Prof. Case,

Thanks for your help - this works perfectly. Thanks also to Dan Roe, who suggested the same thing.

Kind regards,

-----Original Message-----
From: David A Case []
Sent: 01 December 2017 17:41
To: AMBER Mailing List <>
Subject: Re: [AMBER] imin=5 not working in AMBER16?

On Fri, Dec 01, 2017, Paul Mortenson wrote:
> Thanks for your suggestion, unfortunately that has not worked either.
> [Added ". $AMBERHOME/" before each sander command. 14 works
> fine, 16 fails with the same error.]

The problem is the "-r /dev/null" flag in your input. The netcdf code (at least as it is called from imin=5) does not know how to write to a pseudo device (which I guess is a bug, but not one that seems very high priority).

In Amber14, the deafult restart format is ascii (which works ok with /dev/null). In Amber16, the default restart format is netcdf, which doesn't play well with /dev/null.

So, either set ntxo=1 in your input file, or remove the "-r" flag, and just delete the restrt file when you are done.

At least, this solution seems to work for me.

....hope this helps...dac

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Received on Mon Dec 04 2017 - 06:30:04 PST
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