But I see amber.sh in the amber16 directory. The text of the file says:
export AMBER_PREFIX="/opt/amber16"
export AMBERHOME=/opt/amber16
export PATH="${AMBER_PREFIX}/bin:${PATH}"
# Add location of Amber Python modules to default Python search path
if [ -z "$PYTHONPATH" ]; then
export PYTHONPATH="${AMBER_PREFIX}/lib/python2.7/site-packages"
else
export PYTHONPATH="${AMBER_PREFIX}/lib/python2.7/site-packages:${PYTHONPATH}"
fi
Jennifer Muzyka
H. W. Stodghill Jr. and Adele H. Stodghill Professor of Chemistry
Centre College
Danville, KY 40422
jennifer.muzyka.centre.edu
http://web.centre.edu/muzyka
________________________________
From: Jennifer L. Muzyka <jennifer.muzyka.centre.edu>
Sent: Monday, February 26, 2018 9:20:01 AM
To: AMBER Mailing List
Subject: Re: [AMBER] trouble with pdb4amber
When we type that command, we get a message that says
No such file or directory.
Jennifer
Sent from my iPad
> On Feb 25, 2018, at 1:39 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> Hi
>
> Try: source amber.sh
>
> Hai
>
> On Sun, Feb 25, 2018 at 12:18 PM Jennifer L. Muzyka <
> jennifer.muzyka.centre.edu> wrote:
>
>> We are working through the tutorials for AmberTools 17 found in the Amber
>> 2017 manual. We get stuck on the one involving pdb4amber (page 200). When
>> we use the command pdb4amber -i orig.pdb, -o new.pdb —reduce —dry, we get a
>> message that says
>> Traceback (most recent call last):
>> File “/opt/amber16/bin/pdb4amber”, line 6, in <module>
>> from pdb4amber import pdb4amber
>> ImportError: No module named pdb4amber
>>
>> This error message confuses us, as we can see a file named pdb4amber in
>> the amber/bin directory. We’d appreciate any information you can offer
>> about what’s going on. I assume that perhaps I went wrong somewhere in the
>> installation process.
>> Thanks.
>> Jennifer
>>
>>
>>
>>
>> Jennifer Muzyka
>> Stodghill Professor of Chemistry
>> Centre College
>> 600 West Walnut Street
>> Danville, KY 40422
>>
>> jennifer.muzyka.centre.edu<mailto:jennifer.muzyka.centre.edu>
>> http://web.centre.edu/muzyka
>> http://organicers.org
>>
>> 859-238-5413
>> fax 859-236-7925
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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Received on Mon Feb 26 2018 - 07:00:03 PST
