Dear Amber users,
I'm trying to run TI to mutate a residue (Cys->Ser) in a dimer protein
(i.e., 2 chains). The mutation I want to simulate is within chain 1.
I'm also following the tutorial available online:
http://ambermd.org/tutorials/advanced/tutorial9/#sidechain_mini
I have a doubt in the step for the generation of the final topologies and
coordinate files using Parmed (creation of merge_protein and merge_complex)
Since in the example reported in the tutorial, there is only one chain, the
resulting order in the merged coordinate generated by Parmed is:
1) wild type protein
2) TER
3) only the mutated residue
4) TER
5) ligand (only in case of the complex)
6) water + ions
I have just converted the restart file (rst) into a PDB file, by means of
ambpdb to inspect the final order of coordinate and topology files.
However, in my case I have 2 chains, so by following the turorial's script
I obtain this result:
1) wild type protein (chain 1)
2) TER
3) only the mutated residue (SER)
4) TER
5) wild type protein (chain 2)
6) ligand (only in case of the complex)
7) water + ions
Is this correct?
Following the tutorial scheme, my doubt is that I should obtain something
like this, instead:
1) wild type protein (chain 1)
2) TER
3) wild type protein (chain 2)
4) TER
5) only the mutated residue (SER)
6) TER
7) ligand (only in case of the complex)
8) water + ions
Can the order affect the final results of the simulations?
Thank you
Josephine La Sala
Drug Discovery and Development
IIT - Italian Institute of Technology
Via Morego 30, 16163 Genova - Italy
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Received on Wed May 30 2018 - 06:30:03 PDT
