[gmx-users] Force field selection for free Bicarbonate molecules in solution

[Faulkner, Matthew]

Micholas,

I have a protein which has a pore through the centre believed to act as channel for a range of molecules, Bicarbonate is one of them. I want to see if Bicarbonate passes through the channel and what happens as it does. I already have interesting events like this for ions I can add using genion so I want to run the same MDS with Bicarbonate. 

Matthew.
________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [gromacs.org_gmx-users-bounces at maillist.sys.kth.se] on behalf of Smith, Micholas D. [smithmd at ornl.gov]
Sent: 04 September 2015 13:26
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Force field selection for free Bicarbonate molecules in        solution

Matthew,

Quick question, what are you trying to examine with the addition of bicarbonate?

-Micholas

===================
Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Faulkner, Matthew <M.Faulkner at liverpool.ac.uk>
Sent: Friday, September 04, 2015 7:42 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Force field selection for free Bicarbonate molecules in    solution

I am trying to find a suitable force field for using Bicarbonate in an aqueous environment in my MDS. I can't find anything where Bicarbonate has been used this way in gromacs in the literature, does anybody know of a reference for me or have advice on which force filed would be best?

I have run several MDS in the OPLS-AA force field for my protein of interest in solution with water and various ions and they work very well,but I would like to add 150 mM HCO3- into my environment. I have a PDB and TOP file prepared using PRODRG for the HCO3- but I'm not sure if the OPLS-AA force field is suitable for this molecule.

Regards,
Matthew.
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