[gmx-users] rotamers and rings

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 11 16:33:27 CET 2011

abdullah ahmed wrote:
> Hello gromacs users,
> I have asked this question before but perhaps I was not clear enough. I
> noticed that in Gromacs verisons 4.5.3 and 3.3.4 when the initial structure
> has some side chains located very close to each other then after energy
> minimisation they become distorted (for example, Phe ring is not flat, and
> for Leu some hydrogen atoms move away from the rest of the side chain).
> I realize that these problems are probably due very close packing of the
> sidechains in the initial structure.
> But I hope to keep the close contacts in the initial structure and obtain
> correct stereochemistry of the molecule after the minimisation. Is this
> possible?

The outcome of energy minimization is dictated by the functional form of your 
chosen force field and the parameters it assigns to the constituent atoms in 
your structure.  If you're getting unreasonable geometry after EM, then your 
starting structure is physically unreasonable.  You could try to restrain and/or 
freeze these configurations, but I would suspect that any subsequent MD will 
crash instantly when these atoms shear apart from one another.  If the 
configuration is not stable in EM, it will not be stable in MD.


> Sorry for bothering you again and thank you in advance for your help,
> Abdullah Ahmed


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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