Dear David
Thank you for your suggestion. I modified the frcmod, prep and pdb files
(attached) by replacing any OH and HW with OK and HK atom types and
removing all the other atom types (CT, NP, etc). This now brings me a new
question regarding the prep file, why is one of the hydrogen atoms is
described as an "S" while the other two as "E"? to my understanding an "E"
atom is connected to only one other atom while the "S" one has two
connections, Is this because the "S" one here is the first real atom in
connection to the dummy "DU" main atoms? The same difference is observed in
the pdb file as well.
Best
Sam
On Wed, Apr 5, 2017 at 7:51 AM, David A Case <david.case.rutgers.edu> wrote:
> On Tue, Apr 04, 2017, Samaneh Ghassabi Kondalaji wrote:
>
> > I am attempting to perform a simulation that requires Baaden
> hydronium
> > ions in a tip3p water box as provided here:
> > http://research.bmh.manchester.ac.uk/bryce/amber
>
> > Using the frcmod, pdb as well as the prep files provided, the atom
> type
> > definitions as H, OW and HW eventually leads to generation of a prmtop
> > file where the atom type definitions for both H3O+ ions and tip3p water
> > molecules are the same (OW AND HW) although the charge values are
> > distinguished. I was trying to modify the initial force field files for
> H3O
> > by replacing H and HW with H3, but I couldn't find any replacement for
> > OW that matches the amber atom type. Is there any particular atom type
> that
> > can be used to represent the Amber atom type for the O atom in hydronium
> > ion?
>
> You probably want to make up your own atom type: choose a two-letter type
> that is not otherwise being used, and assign the hydronium ion parameters
> to it. (Do the same thing for hydrogen: don't try to re-use an existing
> atom type.)
>
> > Also, Can the addions command in tleap be used to add the hydronium
> > ions inside the box?
>
> Yes. (As far as I know--haven't tried it. AddToBox is another common way
> to add waters and ions around a solute.)
>
> ...dac
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Samaneh ghassabi kondalaji*
*PhD student in Chemistry*
*555 CRL, Chemistry department*
*West Virginia University *
*Morgantown, USA*
*E-mail: **saghassabikondalaji.mix.wvu.edu*
<saghassabikondalaji.mix.wvu.edu>
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- application/octet-stream attachment: H3O_.in
Received on Wed Apr 05 2017 - 09:30:02 PDT
