Dear Justin
I docked a ligand to a hetrodimer protein, I know the approximate
position of the ligand but I don't know whether or not the docked
ligand is relaxed in the binding site or is it taken the proper
orientation? I run the ligand-protein complex for 5ns MD by using
charmm force field and
Hi All
I have tip3p water potential parameters from 3 different sources and they
differ quite substantially. I tried finding answer on the web or manual,
but no success.
Following lists all the three sources and bond potential force constant
(kb) value, in bracket as an example of how values
On Sun, Mar 9, 2014 at 1:00 PM, Chetan Mahajan chetanv...@gmail.com wrote:
Hi All
I have tip3p water potential parameters from 3 different sources and they
differ quite substantially. I tried finding answer on the web or manual,
but no success.
Following lists all the three sources and bond
On 3/9/14, 6:28 AM, jim wrote:
I'm confused about the existence of H5'1 and H5'2 atom names in the RNA
nucleotides (in merge.rtp). I thought all atom names followed the CHARMM 36
atom name convention. Particularly, why do atoms H2' and H2'' correspond to
the latter, while H5'1 and H5'2 carry
Hi Mark,
Thanks for the reply. Now, 1983 article by Jorgensen gives parameters for
rigid tip3p, whereas I am seeking that for flexible tip3p. Force constant
is not mentioned in 1983 article by Jorgensen. The article that I cited in
#1 point below gives these parameters for modified tip3p. I do
Thanks for the clarification.
*Bonds involving H5' and H5'' in RNA residues should indeed be changed to
the H5'1 and H5'2 nomenclature.*
Even though H5' and H5'' are connected to the same atom, what would be the
problem to keep these H atom names H5' and H5'' instead of changing them to
H5'1
Thanks, but I'll have to ask you something again. :)
On Sun, Mar 9, 2014 at 5:00 PM, Justin Lemkul jalem...@vt.edu wrote:
On 3/9/14, 7:23 PM, Jim wrote:
Thanks for the clarification.
*Bonds involving H5' and H5'' in RNA residues should indeed be changed
to
the H5'1 and H5'2
