AMBER Archive (2009)

Subject: Re: [AMBER] loading a mol2 file in xleap

From: FyD (
Date: Fri Jul 24 2009 - 15:00:41 CDT

Dear Jose Luis,

Are you sure the Tripos moL2 file format generated is correct ?

See for instance

If your molecule is too big, you could split it in more elementary elements.

regards, Francois

> I want run a molecular dynamics job with AMBER8, and I have my molecule
> in a mol2 file generated with the Spartan.
> For start the molecular dynamics with the sander I need first a
> coordinate and topology file, and for this purpose I use the xleap.
> For load the mol2 file I use this command:
> LIG=loadmol2 name_of_my_file.mol2
> and I don't obtain any error, but when I use the command "list" the LIG
> residue doesn't appear in the list.
> Why happens this? How can I solve it?
> regards,
> Josť Luis
> P.D.: I know the possibility of generate a prepin file with the
> antechamber, but my molecule is too big for this sub program.

AMBER mailing list