Adding charges to atoms

[stipe.mustac@…]

Hello!

There is an issue when trying to assign partial charges to atoms in a 
pdb file. The error I get is:

/app/bin/amber20/bin/antechamber: error while loading shared libraries: 
libcifparse.so: cannot open shared object file: No such file or directory

Am I doing something wrong or is it a bug? Thank you.

Sincerely,
Stipe Musta\u0107

[Eric Pettersen]

Hi Stipe,

Thanks for reporting this problem. It is a bug, but I don't have access to a Linux machine here at home so I won't be able to investigate further until I'm at work tomorrow. In the interim, if you have any access to a non-Linux machine, you should be able to add charges using that.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[Greg Couch]

antechamber isn't linked against libcifparse.so on Linux, so that error doesn't make sense. Which version of ChimeraX do you have? And what operating system and version are you running it on?

[Eric Pettersen]

Antechamber in turn runs several other programs (bondtype? certainly sqm), so it could be one of the subprograms causing the error.

[stipe.mustac@…]

I am running 1.10.1 ChimeraX on Arch Linux. I am not sure if term 
"version" is applicable to Arch, but I have fully updated system running 
6.17.5 kernel. It could be possible that some subprogram is causing an 
error, but after I got that error I tried to assign charge to a same 
molecule directly using antechamber which worked (using Amber from a 
cluster though, not on my own pc). Besides that, shouldn't flatpak 
installed ChimeraX work the same on every system?

On 10/29/25 5:22 PM, ChimeraX wrote:
>

[Greg Couch]

Yes, the flatpak should be the same everywhere. And that is the difference. It is a bug in the flatpak distribution.

[stipe.mustac@…]

So is there something i can do? I mean I tried downgrading to regular 
Chimera which does the trick, if that is a solution?

On 10/29/25 7:10 PM, ChimeraX wrote:
>

[Greg Couch]

You would need to copy the antechamber from a regular Linux build into the flatpak somehow. We will also get this fixed in the daily build, and let you know when it is available. So a day or two.

[stipe.mustac@…]

Copy the antechamber or the missing library? Either way I can use the 
old Chimera to do the job for the next few days. Thank you very much for 
your assistance.

Am 29.10.2025 um 19:28 schrieb ChimeraX:

[Eric Pettersen]

Seems like a problem with the Flatpak build.

[Greg Couch]

For some reason, the flatpaks are using AmberTools 24 instead of AmberTools 20, like the rest of the Linux builds. And the x86_64 AmberTools 24 tarball is defective. It has the wrong RPATH and doesn't include the libraries. The Linux arm flatpak looks like it would work.

[Zach Pearson]

If I remember right: amber is pretty strict about its compiler. I had to use a newer version of the base flatpak image which necessitated updating amber. 

\u2014 Zach

[Greg Couch]

Zach, do you want to upload a fixed ambertools-24-Linux-Freedesktop-24.08.tar.bz2 or revert to AmberTools 20?

[Zach Pearson]

I\u2019ll upload a fixed tarball. 

\u2014 Zach

[Greg Couch]

Since the updated tarball isn't there yet, I've made a temporary copy of ambertools-20-Linux-CentOS-8.tar.bz2 to ambertools-24-Linux-Freedesktop-24.08.tar.bz2. And then maybe tonight's build will work.

[Greg Couch]

The github workflow didn't pick up on the change. Perhaps because the timestamp wasn't newer. I've touched the tarball, so maybe github will pick it up tonight.

[Zach Pearson]

It has nothing to do with the timestamp on Plato -- if you change the underlying asset but don't rename it and it's not renamed in the consolidated cache's action.yml then GitHub has no idea it needs to invalidate the existing cached asset and re-pull them. I've deleted the ambertools cache so that it will pull on the next run of any of the workflows.

[Greg Couch]

Confirmed that current x86_64 flatpak daily build works.