[gmx-users] Required help in topology making
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
> the cofactor Pyridoxal phosphate. I have created other parameters of
> heteroatom PLP through PRODRG and manual checking. But I am not sure how
> 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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