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.