[gmx-users] Simulation with ligand on protein surface

az adam.zalewski at mail.com
Fri Jul 10 11:03:58 CEST 2015

Hi all

I was wondering if anyone had experience/pointers regarding simulating 
protein-ligand systems where the interface was heavily surface-exposed ?
I've been running quite a few of those these days with Amber99SB--ildn, 
TIP3P, and acpype (i.e. Ambertools) for ligand parametrization, mainly 
for the purpose of probing stability of peptidomimetic docking poses 
(10-50ns; aside from the force-field I follow Justin Lemkul's tutorial 
quite closely). Having however noticed that some of my reference ligands 
(i.e. ones with crystallographic/NMR data) wander away from where they 
should remain, I started wondering whether there could be something 
wrong with my setup. I obviously understand there's a zillion 
possibilities here, but I was still wondering whether there exists some 
sort of 'good-practice' for such cases (e.g. choice of force-fields, 
equilibration protocols ... anything really). I cannot be the only one 
doing this and if anyone has a protocol that served them well in the 
past, I'd love to learn about it.


PS. Links to literature or existing discussions are equally appreciated.

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