Re: [AMBER] Loading .mol2 file in sleap

From: Ben Roberts <>
Date: Wed, 30 Mar 2011 10:43:00 -0400

Hi Rob,

On 30/3/2011, at 9:12 a.m., r smith wrote:

> Hello,
> I am using sleap in AmberTools version 1.4 to create prmtop and inpcrd files
> for use with the amoeba force field. After loading the .mol2 file
> em_ac.mol2 with the command:
> mol = loadmol2 em_ac.mol2
> I receive the following error:
> sleap: data.cpp:276: void mort::mcmpdata_t::set_s(const mort::hashid_t&,
> int, const std::string&): Assertion `absid >= 0 && absid < m_idcounter'
> failed.
> Aborted
> However, the file is loaded without error when using tleap. I have attached
> the .mol2 file. Do you notice anything in the file that would cause sleap
> to fail?

It would appear that the header of your mol2 file (the line between ACT and SMALL, that reads "29 28" etc.) specifies that your molecule contains only one residue - the third number on that line indicates the total number of residues expected (the first two numbers being the number of atoms, and the number of bonds). Atom records, however, refer to two separate residues (ACT and EMM).

Changing that number from 1 to 2 makes the error go away.

Hope this helps,

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Received on Wed Mar 30 2011 - 08:00:03 PDT
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