Re: [gmx-users] Assigning protonation states using Amber ff

2012-01-30 Thread Mark Abraham 

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 listgmx-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

[gmx-users] Assigning protonation states using Amber ff

2012-01-30 Thread Zoe Hall 
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? 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.

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 listgmx-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