Re: [AMBER] Antechamber permissions issue

From: Sam Walsworth (Researcher) <"Sam>
Date: Mon, 30 Nov 2020 10:22:36 +0000

Hi David

my amberhome variable is home/username/amber20_src. With regards to configuring, I'm not entirely sure what I used, the instructions I followed mentioned ./configure gnu and then source ~/.bashrc.

The command line I used was antechamber -i sustiva_new.pdb -fi pdb -o sustiva.mol2 -fo mol2 -c bcc -s 2.

I'm not sure how to run the test suite but I'll have a look round google.

Thank you for the replies
From: David A Case <>
Sent: 27 November 2020 22:10
To: AMBER Mailing List <>
Subject: Re: [AMBER] Antechamber permissions issue

On Fri, Nov 27, 2020, Sam Walsworth (Researcher) wrote:
>Yes I've since realised that the capital letter files are intermediates
>(hence don't exist initially). I tried touch abc and that worked. Is
>it possible that the antechamber program I'm running isn't
>located where I think it is? The error it gives suggests it's at
>/home/username/amber20_src/bin/to_be_dispatched/antechamber but touch abc
>works all over here. Is it possible I've installed it erroneously in a
>different location that doesn't have writing permissions? If so how would
>you check that?

Everything you report looks OK to me. It doesn't matter where the
executable is located: what should matter is the local directory from
which it is invoked.

What is in your AMBERHOME variable? Did you use the old "configure"
script to install? That should be OK, however.

Maybe you should report the command line arguments you used. But I'm
grasping a straws here, since I don't see what would give you the
permissions errors you report.

Of course, if you haven't run the test suite, by all means do so, at
least for the antechamber parts. That might provide some additional


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Received on Mon Nov 30 2020 - 02:30:02 PST
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