[gmx-users] how to add a PTR residue into the gromacs simulations

Mark Abraham mark.abraham at anu.edu.au
Sun Mar 11 12:12:51 CET 2007

> Are there any examples online which I could use as a guide to add the
> residue?  I obtained an .itp file from the HIC-up server for PTR but that
> format seems to differ from the .rtp format. Are there for instance
> scriitps available to make this conversion?

No, this is very much a one-off job that people do, and so nobody has
developed a general program to do it - and it would be a difficult and
thankless task to write one.

Assuming phosphate-suitable parametets exist in the force field, you
should look around the other residues for a phosphate group to copy the
general approach from... sulfate might work analogously too... anyway I've
no idea what phosphotyrosine looks like, so you're on your own really.

If no phosphate parameters exist, then you have a more serious problem.


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