AMBER Archive (2006)

Subject: Re: AMBER: hydronium ion parameters

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Sep 08 2006 - 15:41:17 CDT

Dear MYUNGGI,

I checked out the files, and with those files, I think it is enough to
load the H3O molecule (without doing any kind of manual change). Here is
the xleap.in I wrote to load the structure:
------------- xleap.in -------------
source leaprc.rna.ff99
loadAmberPrep PREPH3O.DAT
loadamberparam ORG1.frcmod
molecule = loadpdb H3O+.pdb
------------------------------------
You can saveoff to create your .lib file if u want. The ORG1.frcmod file
has the missing force field parameters for the structure; so, even though
u will create your .lib file, u will need this .frcmod file whenever u
want to load the structure.

Best,

On Fri, 8 Sep 2006, Myunggi Yi wrote:

> I found one.
>
> http://pharmacy.man.ac.uk/amber/
>
> However, it looks old format which I can't understand.
>
> How can I read or convert to amber 7-9 version?
>
>
>
> On 9/8/06, Myunggi Yi <myunggi_at_gmail.com> wrote:
> > Dear users,
> >
> > Where can I find hydronium ion parameters?
> >
> >
> > --
> > Best wishes,
> >
> > MYUNGGI YI
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
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> >
>
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

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