From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri Jul 21 2006 - 16:49:34 CDT
Hello Anya,
If you're trying to simulate a system that contains non-parameterized
residues, psfgen will keep telling you that some parameters are
missing. I really don't know if somebody from the list has already
worked with the carbohydrate fragment you're interested in. If not,
then you'll need to get both the topology and parameters for your
specific molecule. If you have some experience at parameterizing
residues, you could use the paratool utility included in the latest
version of VMD. Be aware that you'll need also Gaussian for your QM
calculations.
Cheers,
Michel
2006/7/21, a-yermakova_at_northwestern.edu <a-yermakova_at_northwestern.edu>:
>
> 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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