[gmx-users] Peptide drifting and non-natural amino acids

Kirill Bessonov kbessonov at gmail.com
Fri Aug 7 01:45:31 CEST 2009

I was giving today my poster presentation and one of profs from my
department was very critical on the fact that my peptide is drifting or
moving along the DMPC bilayer. Watch video of 100ns simulation here:

He said that is unprobable, I want to know if this is some kind of artifact
(i.e. system is diffusing). I had DMPC molecules displaying artifacts, so I
converted trajectory with
trjconv -pbc mol -ur compact

Another question: I want to start simulation of a pepetide that has
non-natural amino acid (Azetidine -2 - carbpxylic acid, AZE in short). The
only structural difference is that proline has 5 membered ring and AZE only
4. Therefore I was wondering if it is at all possible to simulate that kind
of peptide, since I expect complains from grompp about amino acid name, AZE
not being in its database. Please advise on how to approach this problem

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