Hello all,
Has anyone parameterized Brefeldin A or GDP for Amber force fields? I wish
to simulate a protein with BFA and GDP as ligands, but have so far been
unable to find parameters for these molecules.
I have a procedure to do so using RED and Gamess, but understand this is a
difficult
Ah thank you! This fixed the problem.
Jeremy Todd First
Webb Research Group
University of Texas at Austin
jeremy_fi...@utexas.edu
On Mon, Jul 18, 2016 at 3:31 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 7/18/16 4:27 PM, Jeremy T First wrote:
>
>> Hello,
>>
Hello,
I am attempting to quantify the amount of hydrogen bonding environment a
certain residue experiences during the course of a simulation. To do this,
I am using gmx hbond to plot the number of hydrogen bonds between the
solvent (water) and the hydroxyl oxygen of the residue as a function of
Hi Dilip,
There is quite a bit of literature, especially recently, that considers the
alpha carbon as a hydrogen bond donor. How well this is represented in your
simulation will depend on your force field.
You will likely need to develop your own gromacs tool to calculate this,
but it should be
