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
[email protected]_
--
gmx-users mailing list [email protected]
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 [email protected].
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
