Hello,
I have done calculations using standard GROMOS
43a1 and 53a6 parameters (GROMACS 3.3.3) for a 4-hydroxy-L-proline derivative
(HYP), where the
gamma-OH and the alpha-CO groups are trans to each other in the starting
structure. However, over the course of MD the trans-configuration of these two
substituents changes into a
cis-configuration, which was not supposed to happen. Is there any way to avoid
such isomerisation?
Abil
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