Multiple Chains

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    To do a simulation of multiple topologically distinct chains, we first differentiate two cases - those where the chains are topologically identical, and those where they are not.


    Identical chains

    This is the easy case. Take a structure file with a single chain and use pdb2gmx on it. (Note, as normal, it is not necessary for this structure to be in PDB format.) Take a good look at the resulting .top file, and at the bottom you will see a section like

    [ molecules ] 
    Protein            1

    and earlier this molecule will have been named "Protein" (or whatever). You can just increase that counter from 1 to whatever you require, and then use this .top file with a coordinate file with a corresponding number of chains as input to grompp.


    Non-identical chains

    This is trickier. Now you need to use a structure file that allows you to identify different chains. The PDB format permits you to do this with a letter in column 22. Now you use the -nomerge option to pdb2gmx to require it to recognise different chains as different molecules. Note that in the resulting .top file, any chains that do happen to be identical won't be recognized, and thus you'll have redundancies.

    Page last modified 10:47, 10 Oct 2009 by JLemkul?