AMBER Archive (2008)

Subject: Re: AMBER: problems form the pdb to the mol2

From: David A. Case (
Date: Mon Jun 23 2008 - 20:51:46 CDT

On Tue, Jun 24, 2008, Rilei Yu wrote:
> I came across a problem: when I transform the mol2 format file to the pdb
> format file in sybyl, the type of a "N" atom also change from the Nam
> to the N2 (The only one N atom in the ligand molecule). Then I try to
> change the type of the N in the Sybyl to obtain the original type (Nam),
> unfortunately, I failed.

You don't say exactly *how* you tried to transform the mol2 file to pdb. If I
read your email correctly, you tried to do this "in sybyl". Someone here may
be able to help, but this doesn't (on its face) look like a question that has
anything to do with Amber(?)

If I am misunderstanding your question, you will probably need to be more
explicit about exactly what you tried to do, and what happened.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)