I think I know why I can't not reproduce the error anymore. I am using
MacOS and it does not care care about DNA or dna.
----- Source: /Users/haichit/miniconda3/dat/leap/cmd/leaprc.dna.bsc1
----- Source of /Users/haichit/miniconda3/dat/leap/cmd/leaprc.dna.bsc1 done
Hai
On Tue, Feb 19, 2019 at 3:59 PM Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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 - 17:00:02 PST
