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

Justin A. Lemkul jalemkul at vt.edu
Fri Aug 7 02:15:24 CEST 2009

Kirill Bessonov wrote:
> 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

I would argue that it would be physically unrealistic to see a peptide *not* 
drift along the bilayer.  To compare, use g_msd to calculate the lateral 
diffusion coefficient of both the peptide and the lipids.  If they are 
comparable, the peptide is simply drifting along with the lipids.

> 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

Add AZE to the force field's .rtp and .hdb file, and use pdb2gmx.  It should be 
fairly straightforward to define this residue based on the building blocks 
present in the force field, especially if you're using a Gromos parameter set.


> Thanks
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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