Re: [AMBER] A few issues

From: Paul, Austin <>
Date: Tue, 19 Feb 2019 19:59:42 +0000

Hi Hai,

I had a go at installing from source to see if I could fix it and open a PR, but getting everything set up was taking too long for me. But perhaps this diagnosis will help:

I'm still seeing the old version of the force field in this code of the master branch:

The version of ambertools where I was seeing this issue was based on python2.7, where the "Could not find file .." error you mentioned was raised.
If you disable the temporary directory and have a look at leap.log that is generated, you'll see that same error message in the log, but it is not raised in the python script. I'm not sure what causes the raised error in python2.7 but fails silently in python3+.
Furthermore, in python3+, the test_mutate unit test passes because it relies on the protein import to fix the structure, which succeeds despite the failing dna import.

Hopefully this is helpful!


-----Original Message-----
From: Hai Nguyen <>
Sent: Friday, February 15, 2019 12:52 PM
To: David A Case <>; AMBER Mailing List <>
Subject: Re: [AMBER] A few issues

ah I see. I am actually using pdb4amber in master branch (already has the


On Fri, Feb 15, 2019 at 8:25 AM David A Case <> wrote:

> On Thu, Feb 14, 2019, Hai Nguyen wrote:
> >I think I met the issue
> >before with error message "Could not open file leaprc.dna.bsc1: not
> found""
> >but I can't reproduce it.
> The "DNA" and "RNA" parts of these filenames needs to be capitalized.
> That is, look for leaprc.DNA.bsc1, etc.
> ....dac
> _______________________________________________
> AMBER mailing list
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Received on Tue Feb 19 2019 - 12:00:02 PST
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