[gmx-users] simulation of a non complete structure

Justin A. Lemkul jalemkul at vt.edu
Mon May 9 17:06:50 CEST 2011

Sajad Ahrari wrote:
> dear users
> is it rational to do a simulation on a structure witch is not complete? 
> i mean pdb structure doesn't cover whole of the protein but it's active 
> core domain.
> may be i should be asking this question somewhere else, but i thought 
> some of you may have concerned with such case and in fact i didn't 
> really know where to ask it!

It depends on your aims.  If you can answer the question of interest while still 
neglecting, i.e. missing termini, and you can prove that the missing residues do 
not play any functional role in the dynamics of the active domain, then maybe 
you can simulate it.  But that is a lot of assumptions.  It's certainly been 
done, but it may require lots of justification and prior proof that no ill 
effects will exist.

Note that this only applies to missing termini.  Anything missing within the 
sequence will cause pdb2gmx to fail, and even if you force it without building a 
suitable model, mdrun will fail due to a physically unrealistic simulation.


> thanks in advance!
> sajad


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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