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.gmail.com> wrote:
> > Dear users,
> >
> > Where can I find hydronium ion parameters?
> >
> >
> > --
> > Best wishes,
> >
> > MYUNGGI YI
> > -----------------------------------------------------------------------
> > The AMBER Mail Reflector
> > To post, send mail to amber.scripps.edu
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> >
>
>
>
--
Ilyas Yildirim
---------------------------------------------------------------
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- University of Rochester - -
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- Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
- http://www.pas.rochester.edu/~yildirim/ -
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Received on Sun Sep 10 2006 - 06:07:26 PDT
