VMD-L Mailing List

From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Sat Nov 21 2020 - 01:09:10 CST

I agree with Daniel. I have been using CHARMM-GUI for building glycan-decorated membrane proteins and embedding them in lipid bilayers as well.

It can produce files compatible with NAMD, Gromacs, Amber and few other MD software. The output files are based on CHARMM FF but the website also provides a convertor to convert to Amber format.

Hope that helps.

Regards,
RPS



________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Daniel STERBULEAC <daniel.sterbuleac_at_usm.ro>
Sent: Saturday, November 21, 2020, 11:55 AM
To: manaskohli1_at_gmail.com
Cc: VMD Mailing List
Subject: vmd-l: Glycoprotein simulation answer

Dear Manas,

Have you considered using CHARMM-GUI to build your MD systems? It can handle complex systems and glycoconjugates, it would be interesting to test it with your configurations.

Regards,

Daniel Sterbuleac

Assistant Professor
Stefan cel Mare University of Suceava
720229, 13 Universității Street, Suceava, Romania