Hi Gustavo,

You're right, the lib files are for modifying Amber so that you can simulate glycoconjugates. 

I looked into MDWeb a bit more. They would have to add GLYCAM as an option. However, MDWeb looks to implement AMBER99SB using either Gromacs or NAMD, so adding GLYCAM will come with the usual problems: AMBER scales it's 1-4 interactions and both Gromacs and NAMD handle that, but GLYCAM does not scale it's 1-4 interactions... So to use both GLYCAM and AMBER parameters you need "mixed" scaling. Neither NAMD nor Gromacs can do that afaik and the effects of not doing this will be system specific. 

Marko Wehle of the "Max Planck Institute of Colloids and Interfaces" created a script to properly convert from Amber/Glycam topologies to Gromacs. Perhaps you could contact WebMD about creating and using your own topology files. I can forward you Marko's script if that turns out to be possible.

On top of all those problems, I must warn you that converting from "native" software comes with a lot of extra complexity. It's very easy to make mistakes. If it's possible for you to get AMBER ($500 I believe) and access to computing resources at your institution, that may well turn out easier in the long run.

Good luck,




Oliver

On Mon, Oct 31, 2016 at 1:15 PM, Gustavo Avelar Molina <[log in to unmask]> wrote:
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