[gmx-users] Re: phosphoserine answer (and phosphate related question)
smithgr at cancer.org.uk
Tue Dec 17 20:42:29 CET 2002
> I am having trouble to generate a topology file for a protein which
> contains a phosphoserine residue; Have anyboby already worked with
I made a phosphoserine a little while ago; you can get it from
"ffG43ap" in the topologies/forcefields section of gromacs.org.
I don't think it's too bad, though I've only really used the
I've been working on making ADP/ATP/GDP/GTP nucleotides recently too.
I'm finding I cant' stop the triphosphate groups getting very
distorted with an MG ion there (like an umbrella turning inside out) -
is this normal with highly charged species? At the moment the ion is a
separate molecule; would it be better to bond it explicitly into the
molecule so I can put in Mg-O-P angle terms etc? I'd be interested to
hear if anyone else tried this.
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