Re: Autopsf

From: Peter Freddolino (
Date: Fri Jul 21 2006 - 16:10:39 CDT

Hi Anya,
you probably need to look for topology and parameter files designed for
whatever the specific unparameterized component in your system is (I
assume from your description that it's some sort of glycosylation),
unless it is very similar to something in the sugar topology file.
Searching for '*** charmm topology file' (where *** is your
unparameterized compound) can yield good results. You can also try to
parameterize it with paratool, in which case I can email you a version
of the paratool plugin that should give you a shot) or parameterize it
by hand.

Peter wrote:
> Hello all,
> I'm using the Automatic PSF Builder on a glycoprotein (hemagglutinin). It keeps halting and telling
> me that there are unparametrized components that I cannot seem to parametrize. I also cannot delete
> them for they may be important for the simulation.
> I'm using the following topology files:
> top_all22_prot.inp
> top_all22_sugar.inp
> top_all27_prot_lipid.inp
> Does anyone know of any other topology files I can use that would be useful for parametrizing this
> protein?
> Thank you!
> Anya

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