[buster-discuss] Error "unable to combine"

[ClAuS Flensburg]

Dear Matthew,

On Thu, Sep 24, 2026 at 09:12:38PM +0000, Whitley, Matthew (NIH/NCI) [C] via buster-discuss wrote:
> Hello all,
> 
> I am currently running BUSTER v. 2026-04-2024 on an Apple M3 Pro Mac.  I have encountered an error during refinement that I?ve never seen before.  Refinement starts and appears to run normally, but after the first big cycle I get the following error:
> 
> 
>  ERROR : [run_buster-0077] unable to combine
> 
>          ./01-BUSTER/Cycle-1/FRG.pdb.0 and
> 
>          ./01-BUSTER/Cycle-1/BUSTER.pdb - see
> 
>          ./01-BUSTER/Cycle-1/pdbcmb.log
> 
> 
> 
> 
> 
>  ERROR : [refine-0058] problems in run_buster: see messages
> 
>          above
> 
> 
> pdbcmb.log contains the following:
> 
> 
> /Users/whitleymaj/GPhL/BUSTER_snapshot_20260424/autoBUSTER/bin/darwin/run_buster: line 2322: /Users/whitleymaj/GPhL/BUSTER_snapshot_20260424/autoBUSTER/bin/darwin/pdbcmb: Permission denied
> 
> I have never had issues with permissions when using BUSTER before, although this is the first time I?ve used this particular release.
> 
> Any ideas as to how to overcome this?

Not seen this one before. Does it reproduce if you run the same job again?

What does

 ls -l /Users/whitleymaj/GPhL/BUSTER_snapshot_20260424/autoBUSTER/bin/darwin/pdbcmb

show for the file permissions?
Can you run it manually with

 pdbcmb -h

?

On another note: Is it a setup with a local (macOS) user or a network
(LDAP etc) one: maybe some network hicup made a user account
"disappear", causing the problem?


Regards,

ClAuS & Clemens (for BUSTER Developers)