How to use EOM on glycosylated proteins

[Loki03]

Hello,
I am new to EOM and would like to ask how to use it for glycosylated proteins? I havent found a way to add the glycosylation into the .seg file.
Thank you for any suggestions.

[AL]

I havent found a way to add the glycosylation into the .seg file.

If you mean the sequence file - this wouldn't work.
You may add glycan groups to your structured domains with the ATSAS command-line program GLYCOSYLATION.

[Loki03]

Thank you AL.

Can I then run it in EOM? I tried to run it on my machine but it still asks for a sequence and then doesnt match it to the pdb that I glycosylated with the GLYCOSYLATION program.
Thanks

[AL]

... it still asks for a sequence and then doesnt match it to the pdb that I glycosylated with the GLYCOSYLATION program.

So EOM runs fine with your domain(s) an the sequence before you run GLYCOSYLATION but after you run GLYCOSYLATION it says the sequence doesn't match?

[Loki03]

It doesn't match with the sequence file - my pdb with glycosylation added by a different software or with glycosylation added by the GLYCOSYLATION.
It only runs if I dont specify the glycans at all. It still complaints of mismatch

[Loki03]

Any idea if this can be solved?

[Hayds]

Hi,

the trick to do this is to add the GLYCANS (using the GLYCOSYLATION ATSAS toll for example), but to then split the PDB files of the protein and the attached glycan. Then when EOM asks if there is 'bound DNA' for each rigid body you then provide the glycan PDB file.

Let us know how this works for you.

Cheers,

Haydyn