Re: [AMBER] Error while running antechamber for modified amino acid residue

From: David A Case <>
Date: Sun, 27 Aug 2017 08:57:40 -0400

On Sun, Aug 27, 2017, Rajarshi Roy wrote:

> I have to create lib file for a modified amino acid residue. For that I am
> trying to run the code of *tutorial B5 ("Simulating the Green
> Fluorescent **Protein")
> but i am getting this following error.*
> *antechamber -fi ccif -i CRO.cif -bk CRO -fo ac -o
> -c bcc -at amber

> Welcome to antechamber: molecular input file
> processor.acdoctor mode is on: check and diagnosis problems in the input
> file.antechamber: mmcif.c:70: rmmcif: Assertion `col2 >= 0' failed.Aborted
> (core dumped)*

Can you post your CRO.cif file? The code is looking to see if this is a
LINKING type residue, but cannot find a "type" column.

When I extract the CRO.cif file from components.cif, I don't see the error
you report.

You could also try commenting out the block starting at line 68
of mmcif.c (in AmberTools/src/antechamber) that exits for linking residues.
Type "make install" in that directory, then re-run you job.

I think we need to add a flag that allows LINKING residues to be processed.


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Received on Sun Aug 27 2017 - 06:00:06 PDT
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