AMBER Archive (2007)

Subject: AMBER: Question about loadMol2

From: David LeBard (david.lebard_at_asu.edu)
Date: Tue Mar 27 2007 - 12:31:56 CST

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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