[gmx-users] [gmx-developers] GMX outputs GLY sidechain as Hydrogen L- or D-

Justin Lemkul jalemkul at vt.edu
Fri Mar 1 20:50:21 CET 2019

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.

On 3/1/19 2:43 PM, Henry Wittler wrote:
> 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.
> 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.

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).

So with respect to your question copied below, VMD is behaving correctly 
- HA1 is the "sidechain" hydrogen.


> This causes a very minor discrepancy in my analysis of insulin 
> systems, however I went past it somewhat awkwardly with vmd commands:
> atomselect macro scGLY {name HA2}
> atomselect macro mcGLY {name H1 H2 H3 HN HA1}
> Best regards (bästa hälsningar),
> Henry Wittler
> /Good day./
> /
> /
> /Thanks for the good software, I use it for my extensive Insulin 
> simulation analysis, using gromacs v.5.0.4. charmm 36.
> Just reporting what I think is a bug in vmd 1.9.3.
> /
> /The glycine HA1, and HA2 appears correctly when selecting the atoms 
> on vmd-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./
> /
> /
> /To compare with the insulin PDB I compare with it uses HA2 for the 
> backbone hydrogen and HA3 for the sidechain hydrogen./


Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129


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