Hi everyone,
I want to call your attention to what appears to be a bug introduced
into Antechamber at some point after the Tutorial A26 "Simulating the Green
Fluorescent Protein and Building a Modified Amino Acid Residue" was written.
I was trying to follow BasicTutorial A26 (
https://ambermd.org/tutorials/basic/tutorial5/index.php). However, right in
Section 2, were we are supposed to derive parameters for the 'CRO' residue,
the command fails as below:
```
$ antechamber -fi ccif -i CRO.cif -bk CRO -fo ac -o cro.ac -c bcc -at amber
Info: acdoctor mode is on: check and diagnose problems in the input file.
Info: The atom type is set to amber; the options available to the -at flag
are
gaff, gaff2, amber, bcc, abcg2, and sybyl.
antechamber:
/home/case/miniforge3/conda-bld/ambertools-dac_1763136447595/work/AmberTools/src/antechamber/mmcif.c:65:
rmmcif: Assertion `col6 >= 0' failed.
~/.conda/envs/AmberTools25/bin/antechamber: line 9: 2388427 Aborted
(core dumped) "$AMBERHOME/bin/wrapped_progs/antechamber" "$."
```
This is the exact command in the tutorial, using the `CRO.cif` file
downloaded directly from the tutorial page. I also tried downloading the
CRO.cif file from RCSB (
https://rcsb.org/ligand/CRO), and using Antechamber
from either AmberTools25 or 26, and got exactly the same error every time.
I know this issue has been raised before in the thread here (
http://archive.ambermd.org/202503/0031.html), but the answer there doesn't
really address what seems to be some bug introduced in Anberchamber after
the tutorial was written.
Has anyone else here hit this error? Are there any suggestions?
Thanks,
--
Gustavo Seabra.
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Received on Fri Oct 09 2026 - 10:30:06 PDT
