AMBER Archive (2004)

Subject: Re: AMBER: Loading mol2 Files in XLEaP

From: David A. Case (
Date: Thu Jun 03 2004 - 17:02:07 CDT

On Thu, Jun 03, 2004, Robyn Ayscue wrote:

> Hi! I'm using Amber 8 on an SGI machine running Irix
> 6.5, and I've been having a bit of trouble with xLEaP
> regarding the "loadmol2" command mentioned in the
> manual. I've tried to load a file by entering the
> following commands:
> variable = loadmol2 "test.mol2"
> variable = loadmol2 test.mol2
> loadmol2 test.mol2
> With each of them I get "syntax error" back from the
> program, and the file fails to load. The file is
> located in the same directory I'm running the program
> from. Also, if it makes any difference, the file is a
> canonical B-conformation T:A 15-residue
> oligonucleotide (DNA). Has anyone else had this
> problem? If so, how did you fix it? Any help would be
> appreciated.

My best guess is that you might still be running xleap from an earlier
version of amber. Is that possible? Be sure that your AMBERHOME variable
is set correctly.

In addition, be careful with a multiple-residue mol2 file; the loadMol2
command was primarily written to read single residue files (say as output from
antechamber). The recommended way to get DNA coordinates into LEaP is to use
loadPdb. We will be working in the future to make the loadMol2 command better
for more than just single residues.

...good luck...dac

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