Re: [AMBER] Topological error for Mg in .prepin file.

From: David Case <>
Date: Thu, 25 Oct 2018 00:58:31 +0000

On Wed, Oct 24, 2018, Anuja Ware wrote:

> I am trying to generate a .lib file (parameters) for a non-standard
> residue, bacteriochlorophyll a. I have optimized the ring structure and
> derived RESP charges. Then I have run antechamber to generate .prepin
> file. But in prepin file the topological parameters of Mg atom are not
> clear. I get an error as follows:
> Atom X: Illegal chain specifier [0] in PREP file.
> 82 X 1 0 1 7.519 nan 0.000 0.000000
> What should one do in such type of case?

Antechamber is not set up to handle metal ions; if you have a recent
version of AmberTools, it should tell you that.

But try this: ask for a mol2 file rather than a prepi file: it doesn't
try to create a tree structure for the molecule. You'll probably still
have to do some hand-editing, but it's much easier to see what is going
on with the mol2 format than with prepi.


AMBER mailing list
Received on Wed Oct 24 2018 - 18:00:02 PDT
Custom Search