AMBER Archive (2009)

Subject: RE: [AMBER] adding MG2 problem

From: Rausch, Felix (frausch_at_ipb-halle.de)
Date: Wed Feb 04 2009 - 07:04:51 CST

Hi,

I already worked with MG2-ions without any trouble. I usually start leap with
the leaprc.ff03 and additionally load in the gaff-parameters with "source
leaprc.gaff" in leap. Also u have to make sure that the ions have the name
"MG2" in the pdb-file. I hope that helps...

With kind regards
Felix Rausch

-----Original Message-----
From: amber-bounces_at_ambermd.org on behalf of Scott Brozell
Sent: Tue 2/3/2009 8:09 PM
To: AMBER Mailing List
Cc:
Subject: Re: [AMBER] adding MG2 problem
Hi,

On Fri, 30 Jan 2009, balaji nagarajan wrote:

> I have tried to generate prmtop and inpcrd files using
> a PDB which has MG2 .
>
-----------------------------------------------------------------------------
-
> Loading PDB file: ./mg_dec2.pdb
> Created a new atom named: MG2 within residue: .R<MG2 41>
> Added missing heavy atom: .R<MG2 41>.A<MG 1>
...
> total atoms in file: 812
> Leap added 456 missing atoms according to residue templates:
> 4 Heavy
> 452 H / lone pairs
> The file contained 4 atoms not in residue templates
>
-----------------------------------------------------------------------------
----------------
> saveamberparmtop command
> the MG2 error came as
>
-----------------------------------------------------------------------------
-----------------
> FATAL: Atom .R<MG2 41>.A<MG2 2> does not have a type.
...
> Failed to generate parameters
> Parameter file was not saved.
>
>
-----------------------------------------------------------------------------
----------------

Did you load the appropriate ions library ? E.g.
loadoff ions94.lib

See these for many more details:
http://archive.ambermd.org/200807/0142.html
http://archive.ambermd.org/200807/0433.html

Scott

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