[gmx-users] missing residues

nunolf at ci.uc.pt nunolf at ci.uc.pt
Thu Apr 6 20:52:16 CEST 2006

Quoting Jayant James Jayasundar <jayant_jacques at rediffmail.com>:

> Hi friends!
> Part of a molecule that I am trying to simulate is not 
> crystallographically resolved. To be exact about 17 amino acids from 
> 136-148.


Are those  residues in the Nter/Cter ? If they are, perhaps leaving the 
without them would be my first approach. The decision could pass by "knowing"
what's the biological relevance of those residues on the whole protein

If they are not terminal residues, then you could try to add them with a
molecular modeling program like (though 17 residues is a big chunk):
swisspdb viewer, jackal, PLOP ...

Best regards,

Please suggest suggestions on how? I go about building these
> missing residues and integrating with the crystallographically 
> resolved structure such that I can proceed with MD simulations.
> Thanks
> Jayant
> Jayasundar Jayant James
> Postdoctoral research fellow,
> Department of Veterinary and Comparative Anatomy, Pharmacology and 
> Physiology(VCAPP), Washington state university, Pullman 99164-6520, 
> USA.
> http://www.chick.com/reading/tracts/0001/0001_01.asp

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