Re: AMBER: Question about loadMol2

From: David Mobley <>
Date: Tue, 27 Mar 2007 13:15:26 -0700

Usually this happens when there is some sort of problem with your mol2
file. LEAP can be slightly finicky sometimes. Try comparing your mol2
file with one that works and looking for differences.


On 3/27/07, David LeBard <> wrote:
> Hi All,
> I am having a problem with the loadMol2 command in xleap from Amber version
> 9. Basically, when I try to load a molecule from a mol2 file (generated by
> VMD), I get no errors but the unit is not created. So, whenever I do an
> edit, desc, or check on my unit, xleap says my molecule doesn't exist.
> The reason I am doing this is because I want to preserve my molecule's
> bonds, which are killed when I try loading my molecule from a PDB file into
> leap. Any suggestions?
> Many thanks in advance,
> David
> ************** From xleap
> **********************************************
> > bph = loadmol2 bph.mol2
> Loading Mol2 file: ./bph.mol2
> Reading MOLECULE named bph
> > check bph
> check: Argument #1 is type String must be of type: [unit molecule residue
> atom]
> usage: check <unit> [parmset]
> ************** End From xleap
> *****************************************
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Received on Wed Mar 28 2007 - 06:07:45 PDT
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