Re: [AMBER] Help regarding Mn parameters

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Fri, 7 Jun 2013 15:02:29 -0600

Hi,

On Fri, Jun 7, 2013 at 12:07 PM, Mallipeddi, Premalatha
<Premalatha.Mallipeddi.stjude.org> wrote:
> mods = loadAmberParams "frcmod.Mn" which I downloaded from http://www.pharmacy.manchester.ac.uk/bryce/amber#ion

There should probably also be a prep or OFF file in addition to the
frcmod file, e.g. something like:

parmmg = loadamberparams frcmod.magnesium
loadamberprep magnesium.prep

> The pdb file has only protein and MN atoms. Mn atom coordinates are as follows:
> HETATM 1520 MG+ MG+ D 303 -14.664 -20.531 -22.254 1.00 59.85 MG2

I'm a little confused here - you say you need manganese parameters but
you've pasted the coordinates of what appears to be a magnesium ion.

-Dan

-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jun 07 2013 - 14:30:03 PDT
Custom Search