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On 1/09/2011 6:14 PM, Steven Neumann wrote:
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cite="mid:CAKZJqQEScmYc8OHCCTHt6_N7DS3j-crifVBesktiC3R_scTsDA@mail.gmail.com"
type="cite"><br>
<br>
<div class="gmail_quote">On Wed, Aug 31, 2011 at 5:54 PM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
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MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im"><br>
<br>
Steven Neumann wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex;
MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">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.<br>
How about other amino acids and their maximum hbonds they
can create?<br>
<br>
</blockquote>
<br>
</div>
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.<br>
<br>
-Justin<br>
</blockquote>
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<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex;
MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">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) :</blockquote>
<div> </div>
<div><em><strong>Reading file md.tpr, VERSION 4.5.4 (single
precision)<br>
Specify 2 groups to analyze:<br>
Group 0 ( r_96) has 7 elements</strong>
-</em> this is my Glycine - 7 atoms (side chain - Hydrogen)<br>
<em><strong>Group 1 ( LIG) has 510 elements</strong>
-</em> these are 10 ligands, 51 atoms each, 8 OH group<br>
<em><strong>Select a group: 0 1<br>
Selected 0: 'r_96'<br>
Select a group: Selected 1: 'LIG'<br>
Checking for overlap in atoms between r_96 and LIG<br>
Calculating hydrogen bonds between r_96 (7 atoms) and LIG
(510 atoms)<br>
Found 81 donors and 112
acceptors </strong></em></div>
<div><strong><em></em></strong> </div>
<div><em>81 donors? It should be 80 when I have 10 ligands with
8 Oh group... Am I right?</em></div>
</div>
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<br>
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.<br>
<br>
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cite="mid:CAKZJqQEScmYc8OHCCTHt6_N7DS3j-crifVBesktiC3R_scTsDA@mail.gmail.com"
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<div class="gmail_quote">
<div><em>112 acceptors? 7 atoms of my Glycine x 12
possibilities?</em></div>
</div>
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<br>
Methylene atoms cannot accept hydrogen bonds! See g_hbond -h. N and
O from glycine are acceptors. 112 = 2*1 + 11*10<br>
<br>
Mark<br>
<br>
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cite="mid:CAKZJqQEScmYc8OHCCTHt6_N7DS3j-crifVBesktiC3R_scTsDA@mail.gmail.com"
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<div class="gmail_quote">
<div><strong><em></em></strong> </div>
<div><em><strong>trn version: GMX_trn_file (single precision)<br>
Reading frame 0 time 0.000<br>
Will do grid-seach on 11x11x11 grid, rcut=0.35<br>
Last frame 2000 time 100000.000<br>
Average number of hbonds per timeframe 0.642 out of 4536
possible - </strong>that is understood = (112x81)/2</em></div>
<div><em></em> </div>
<div><em>So how many possibilities has Glycine in order to
create hbond? Shall I choose just a side chain which is
hydrogen?</em></div>
<div><em></em> </div>
<div><em>Steven</em></div>
<br>
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