[gmx-users] query regarding missing residues

[sonali dhindwal]

Hello Sir,

I want to ask a question about missing residues, for which coordinates are not defined in the PDB file.
I have this protein structure and in one of the loop there are some residues whose coordinates are not defined in the file.
When I did pdb2gmx for preparing the topology, it joined the end of this loop and renumber ed the whole chain there after.
I searched on net and it was written that missing residues should be modelled somehow before running simulation, but in my case i cant model this loop having missing residues because these are very flexible and i cant define their coordinates through modeling,
So, if there is someway through which these residues remain missing and still I can go ahead with simulation ?
Thanks in advance.
Regards

--
Sonali Dhindwal

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