Re: [AMBER] Antechamber permissions issue

From: Sam Walsworth (Researcher) <"Sam>
Date: Mon, 30 Nov 2020 11:23:56 +0000

Hi David

It's actually running now. I used the stat command on that empty intermediate file, realised it was from before I modified write permissions in relevant directories so I removed it and re ran. Now it works. Was just a write-permission issue.

Thank you for the help

From: Sam Walsworth (Researcher) <>
Sent: 30 November 2020 10:48
To: AMBER Mailing List <>
Subject: Re: [AMBER] Antechamber permissions issue

It's also worth noting that despite the antechamber function not going through for whatever reason, it did seem to create the ANTECHAMBER_BOND_TYPE.AC0 intermediate file in question. It appeared in my home/username/amber20_src folder (which is my $AMBERHOME) and when I tried to remove it out of interest it gave me the following message:

rm: remove write-protected regular empty file 'ANTECHAMBER_BOND_TYPE.AC0'?

Somewhere the antechamber program is running out of a write-protected location it seems.

From: Sam Walsworth (Researcher) <>
Sent: 30 November 2020 10:22
To: AMBER Mailing List <>
Subject: Re: [AMBER] Antechamber permissions issue

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 - 03:30:02 PST
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