Re: [AMBER] Problems with tleap when generating gib structures

From: Levan Tsereteli <>
Date: Tue, 5 Jan 2016 14:26:07 +0000

Hi David

Thanks a lot for the response.
i tried what you suggested but it does not work. Fails again with segmentation fault. As it seems tleap has indeed a limit on the number of sequence units and its located at AmberTools/src/leap/src/leap/xaLeap.rm4 file under the variable "XaLeap*$1Table.$1Data.min: 120" So its allowing to build structures with a bit more then 120 units. I am gonna change that value and recompile ambertools lets see what happens.


From: David A Case []
Sent: 05 January 2016 14:25
To: AMBER Mailing List
Subject: Re: [AMBER] Problems with tleap when generating gib structures

On Tue, Jan 05, 2016, Levan Tsereteli wrote:
> I am facing very strange problem when using tleap. Just want to generate
> .crd, mol2 and prmtop with tleap but whenever system that I want to
> build is bigger then 125 units its giving me segmentation error.

What happens if you leave out the "saveMol2" parameter? Amber's mol2 support
is mainly for single residues, and there may be problems with mulitple-residue
mol2 processing. Or, there may be limits on the sequence command.

Generally, it would be great to know *when* the segfault is happening.

What happens if you add a savePdb command (and nothing else) right after
the sequence command? Do you get a reasonable PDB file?


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