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

[Henry Wittler]

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.
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.*
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