[gmx-users] Required help in topology making

Mark Abraham Mark.Abraham at anu.edu.au
Wed Jul 29 10:00:32 CEST 2009

supti mukherjee wrote:
> Dear All
>    I have a protein where one residue ( Lysine ) is making a covalent bond
> with
>    the cofactor Pyridoxal phosphate. I have created other parameters of
>    heteroatom PLP  through PRODRG and manual checking. But I am not sure how
> to
>    include the parameters for the "imine" bond ( C=N  bond ) that has been
>    formed between side chain amine group of lysine and aldehyde group of
>    Pyridoxal phosphate.
>    Do I have to edit  C-termini database file ( ff????-c.tdb ) ?

No, that's only useful for tweaking things along the peptide backbone.

Simplest, if you already know what you are doing, is to edit the .rtp 
file to make a modified lysine residue that has the cofactor with all 
the right parameters. Then pdb2gmx can just work on a structure you 
provide that has the cofactor. Detailed knowledge of chapter 5 of the 
manual will be required.

As a guide, you might construct a cofactor-bound lysine, and give that 
to PRODRG and use the topology generated as a partial template for the 
modified lysine residue. Perhaps work on a H2C=N lysine modification 
first of all, and then scale up.

Whether PRODRG generates suitable parameters is something you will have 
to verify independently.


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