Hi, I suggest taking a look in RED.DB web site (http://q4md-forcefieldtools.org/REDDB/index.php), where some RESP charges for DNA are stored.
HTH Stephane ---------------------------------------------------------------------- Message: 1 Date: Tue, 31 Jan 2012 16:11:02 +1100 From: Mark Abraham <mark.abra...@anu.edu.au> Subject: Re: [gmx-users] Assigning protonation states using Amber ff To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <4f2777e6.9030...@anu.edu.au> Content-Type: text/plain; charset="iso-8859-1" On 30/01/2012 11:30 PM, Zoe Hall wrote: > > Dear gromacs users, > > I am carrying out solvent-free simulations of a DNA-protein complex > using the Amber forcefield. Amber automatically assigns negative > charges to the DNA. Is there any way to have neutral DNA? > Probably not, but you would have to consult the AMBER force field documentation (i.e. published papers) for an initial answer. > Similarly, I would like to select which Arg residues are protonated, > however the Amber forcefield does not appear to support deprotonated > Arg. Is there any way around this? Previously I have been able to > assign the protonation state of all basic and acidic residues with the > OPLS forcefield (using the interactive commands in pdb2gmx), however > with DNA included, I figured I needed to use Amber. > Different force fields are different. If neutral arginine is correct for your system, then you will have to parametrize and make a new .rtp entry accordingly. Mark > Any advice on this would be appreciated! > > Thanks in advance, > > Zoe Hall > > Zoe Hall > > Department of Chemistry > > Oxford University > > _zoe.h...@chem.ox.ac.uk_ > > > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
