[gmx-users] ffamber ports for 3.3.1

[Eric J. Sorin]

> Has the problem with the terminal hydrogen in nucleic acids been solved?

Hi Maik,

As discussed on the ffamber website, there are several ways to deal with this, the most simple of 
which is to not include NA residues in the aminoacids.dat file (during pdb2gmx importing), so this 
is not really a problem anymore.  Thanks.

Eric J. Sorin
Pande Group
Stanford University
http://folding.stanford.edu/ffamber/

> Eric J. Sorin wrote:
> Hello GMX users,
>  Our AMBER ports for gromacs have just been extended to include new version 3.3.1.  For those 
> simulating nucleic acids, this is a nice change, as 3.3.1 supports a new .hdb format that will 
> allow use of hydrogen database files for nucleic acids.  Please download from the website below. 
> Thanks!
>  Eric J. Sorin
> Pande Group
> Stanford University
> http://folding.stanford.edu/ffamber/