On 1/09/2011 6:14 PM, Steven Neumann wrote:
On Wed, Aug 31, 2011 at 5:54 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Steven Neumann wrote:
One question.... for Glycine it is easy to assess 3 possible
hbonds which can create as hydrogen is only one atom as a side
chain.
How about other amino acids and their maximum hbonds they can
create?
Any OH or NH group is a donor, any lone pair is an acceptor
(though obviously not modeled explicitly in MD). The ability of
MD force fields to agree with reality in this respect is
debatable, but should come close.
-Justin
Thank you Justin. Can you please clarify me something and tell me
whether I am wrong. This is what I obtained from calulating hbonds
between 10 ligands and Glycine. Each ligand serve 8 OH group
(flavanoid) :
/*Reading file md.tpr, VERSION 4.5.4 (single precision)
Specify 2 groups to analyze:
Group 0 ( r_96) has 7 elements* -/ this is my
Glycine - 7 atoms (side chain - Hydrogen)
/*Group 1 ( LIG) has 510 elements* -/ these are 10
ligands, 51 atoms each, 8 OH group
/*Select a group: 0 1
Selected 0: 'r_96'
Select a group: Selected 1: 'LIG'
Checking for overlap in atoms between r_96 and LIG
Calculating hydrogen bonds between r_96 (7 atoms) and LIG (510 atoms)
Found 81 donors and 112 acceptors */
*//*
/81 donors? It should be 80 when I have 10 ligands with 8 Oh group...
Am I right?/
You are assuming g_hbond knows what you know - that only your ligand
hydroxyls can do effective H-bonding. However, g_hbond can only look at
the atom names of the groups you give it. Algorithms do what you say,
not what you mean, unfortunately. 81 = 1*1 + 8*10, since NH from glycine
is a donor.
/112 acceptors? 7 atoms of my Glycine x 12 possibilities?/
Methylene atoms cannot accept hydrogen bonds! See g_hbond -h. N and O
from glycine are acceptors. 112 = 2*1 + 11*10
Mark
*//*
/*trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
Will do grid-seach on 11x11x11 grid, rcut=0.35
Last frame 2000 time 100000.000
Average number of hbonds per timeframe 0.642 out of 4536
possible - *that is understood = (112x81)/2/
//
/So how many possibilities has Glycine in order to create hbond? Shall
I choose just a side chain which is hydrogen?/
//
/Steven/
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