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<tt>As this is not an issue actually related to GROMACS developing,
I am copying it over to the gmx-users mailing list; please
continue any discussion there.</tt><br>
<br>
<div class="moz-cite-prefix">On 3/1/19 2:43 PM, Henry Wittler wrote:<br>
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cite="mid:CADoE1i0qBTsgM5oPAB--E3E-3q8ZLUf8MsXJQqxzdPB5R98Dgw@mail.gmail.com">
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<div dir="ltr">Good day. In case this is not a trivial question.
I've mainly used gmx charmm36 (mars 2014) force-field. I
emailed this potential issue to VMD directly before, haven't
received reply. Made me wonder if GMX correctly outputs the
sidechain of GLY as a L-amino acid, since vmd reads the
sidechain as the CA-atom of GLY. <br>
A minor change in the topology files should fix this, however
just wanted to alarm in case this is an overlooked issue with
most force-fields.<br>
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The CHARMM force field defines HA2 as being in the analogous
position to HA in other amino acids, and HA1 in the orientation of
where CB would normally be. Perhaps this is a bit counterintuitive,
but given that the glycine CA is achiral, there is no functional
problem with this convention (it comes entirely from CHARMM and
actually has nothing to do with GROMACS at all).<br>
<br>
So with respect to your question copied below, VMD is behaving
correctly - HA1 is the "sidechain" hydrogen.<br>
<br>
-Justin<br>
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<blockquote type="cite"
cite="mid:CADoE1i0qBTsgM5oPAB--E3E-3q8ZLUf8MsXJQqxzdPB5R98Dgw@mail.gmail.com">
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<div dir="ltr">This causes a very minor discrepancy in my
analysis of insulin systems, however I went past it somewhat
awkwardly with vmd commands:<br>
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<div dir="ltr">atomselect macro scGLY {name HA2}
<div>atomselect macro mcGLY {name H1 H2 H3 HN HA1}</div>
<div><br>
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<div>Best regards (bästa hälsningar),<br>
Henry Wittler</div>
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<div><i>Good day.</i></div>
<div><i><br>
</i></div>
<div><i>Thanks for the good software, I use it for my
extensive Insulin simulation analysis, using gromacs
v.5.0.4. charmm 36.<br>
<br>
Just reporting what I think is a bug in <span
class="gmail-il">vmd</span> 1.9.3.<br>
<br>
</i></div>
<div><i>The glycine HA1, and HA2 appears correctly when
selecting the atoms on <span class="gmail-il">vmd</span>-window
(confirming with L/D configuration). However when
using atom-selection with macro 'sidechain' it chooses
HA1 of glycines, however HA2 I believe is the correct
sidechain.</i></div>
<div><i><br>
</i></div>
<div><i>To compare with the insulin PDB I compare with it
uses HA2 for the backbone hydrogen and HA3 for the
sidechain hydrogen.</i></div>
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<pre class="moz-signature" cols="72">--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
<a class="moz-txt-link-abbreviated" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a> | (540) 231-3129
<a class="moz-txt-link-freetext" href="http://www.thelemkullab.com">http://www.thelemkullab.com</a>
==================================================
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