I guess the problem is the naming of residues. In your 1GMO pdb file all the glucosamine residues are label as SGN and all iduronic as IDS. Glycam has different ways of naming these, depending on what is their state. You have to take a look to the files Docs_Glucosamine and Docs_uronic_acids, which you will find in the same page where you found the special parameters, and name the SGN/IDS residues according to them. You can also take a look at https://glycam.org/docs/forcefield/glycam-naming-2/index.html. There are also some issues that you have to take into account with sulphated residues (https://glycam.org/docs/help/2014/04/04/sulfating-glycam-residues/index.html)

All together it might be a bit tricky and it will require some work to have everything fine for tleap.
I do not know, but maybe somebody else can suggest some alternative way to do this.

Jordi


-----Mensaje original-----
De: Robin Singh <[log in to unmask]> 
Enviado el: miércoles, 19 de abril de 2023 16:51
Para: [log in to unmask]; Jordi Bujons <[log in to unmask]>
Asunto: Re: Glycans not recongnized in tleap

Hello Jordi,

Thank you so much for the help, I tried the things you suggested but it did not work and still I am getting the same errors.

If you know about any other way then please let me know.

Regards,
Robin