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-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Smith, Micholas D. [smit...@ornl.gov] Sent: 04 September 2015 13:26 To: gmx-us...@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-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Faulkner, Matthew <m.faulk...@liverpool.ac.uk> Sent: Friday, September 04, 2015 7:42 AM To: gromacs.org_gmx-users@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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.