Hi all,
I'm starting a MD project using gromacs and we're looking to expand on the
previous work in the lab modelling our receptors of interest by looking at the
effects of gylcosylation. Is there a current best standard for parameters for
modelling glycans?
Thanks,
--
Gromacs Users mailing
Hi,
I'm trying to simulate the dynamics of glycosylated proteins using gromacs
4.6.5 and have acquired forcefield parameters from PTM-Vienna (ffG45a3(v1.6)
and ffG54a7(v1.7)) and CHARMM-GUI (36-jun2015) that supposedly allow for
analysis of PTMs but both result in a fatal error when trying to
While running the npt step gromacs encountered the following error about 4-6ps
before the end of the mdrun:
File input/output error:
npt_step46830.cpt
I tried the commands for extending the simulation but these seem setup for the
production runs as it quite complaining about the lack of
Hi,
So on Gromacs 4.6.5, I'm using the make_ndx command to try to create a custom
index of a binding pocket on my protein of interest, I want to group 5
non-contiguous residues, I can index them separately and tried to group them
with & but that creates an empty group error because I guess it