Gromacs

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.

    You can use editconf to create translated copies of the chains to concatenate later in a single file.

    Non-identical chains

    This is trickier. Now may to use a structure file that allows you to identify different chains, such as the PDB format, which permits you to assign a letter in column 22.  The pdb2gmx program can recognize different chain identifiers, and will write them as different molecules (and thus to separate topologies).  For instance, chain A will correspond to a topology named topol_A.itp, chain B will be topol_B.itp, etc.  Note that in the resulting .top file, each chain will be written as a separate topology, even if the chains actually represent identical molecules (i.e., a homodimeric protein).

    Note that it is not necessary to use separate chain identifiers to conduct simulations or to run analysis in GROMACS.  You can create an index file with residue numbers that specify the chains in terms of their numbered residues.  For example, if you have a dimeric protein with each chain consisting of 200 amino acids, chain A might correspond to residues 1-200, and chain B 201-400.  Thus, at the make_ndx prompt, you can enter

    r 1-200
    
    for the first chain, and
    r-201-400
    
    for the second chain.  This way, you can conduct analysis on each chain separately without worrying out chain identifiers.
    Page last modified 14:06, 14 Oct 2009 by JLemkul?