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Hi Oliver,

Thank you for your reply.

I've already taken a look at these files. There are three different .lib
files (amino, aminont and aminoct), and I don't know which one I should
choose. I've read that they're related to glycoproteins, so I got even more
confused. And in these files I couldn't find a .frcmod file, unless it has
a different extension... Any ideia?

Best regards,

Gustavo

Em seg, 31 de out de 2016 às 11:48, Oliver Grant <[log in to unmask]>
escreveu:

> Hi Gustavo,
>
> I haven't used MDWeb, but you can find lib files in the download on the
> parameters page:
>
> http://glycam.org/docs/forcefield/parameters/
>
> Note tgz and zip are just two different compressed files. Pick one you can
> open and I guess go with regular GLYCAM when using AMBER-99SB, not the EP
> version.
>
> Best,
>
> Oliver
>
> On Mon, Oct 31, 2016 at 11:28 AM, Gustavo Avelar Molina <
> [log in to unmask]> wrote:
>
> Dear all,
>
> I would like to know if it is possible to use the GLYCAM parameters to run
> MD simulations using MDWeb (http://mmb.irbbarcelona.org/MDWeb//index.php).
> I have a protein-polysaccharide complex that I want to simulate using this
> server and the AMBER-99SB* force field. MDWeb asks a .lib and .frcmod file
> for my polysaccharide in order to be able to simulate it (
> http://mmb.irbbarcelona.org/MDWeb//help.php?id=checkingLig). However, I'm
> not sure how I can obtain these files from GLYCAM parameter files.
>
> Any ideia is welcome.
>
> Best regards,
>
> Gustavo
>
>
>