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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:


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