Ah you’ right. I need to fix that line too.
Thanks.
Hai
On Tue, Feb 19, 2019 at 2:59 PM Paul, Austin <Austin.Paul.wyss.harvard.edu>
wrote:
> 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:
> https://github.com/Amber-MD/pdb4amber/blob/dd8e274785e16f0017035a57cdd19ec2e976eae6/pdb4amber/pdb4amber.py#L160
>
> 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!
>
> Best,
> Austin
>
>
> -----Original Message-----
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Friday, February 15, 2019 12:52 PM
> To: David A Case <david.case.rutgers.edu>; AMBER Mailing List <
> amber.ambermd.org>
> Subject: Re: [AMBER] A few issues
>
> ah I see. I am actually using pdb4amber in master branch (already has the
> fix:
>
> https://github.com/Amber-MD/pdb4amber/blob/dd8e274785e16f0017035a57cdd19ec2e976eae6/pdb4amber/template.py#L3
> )
> with
> AT18.
>
> Hai
>
> On Fri, Feb 15, 2019 at 8:25 AM David A Case <david.case.rutgers.edu>
> 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
> >
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Received on Tue Feb 19 2019 - 13:00:03 PST
