[gmx-users] Choosing Parameter values of PTMs
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 list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] fatal error trying to simulate glycosylated proteins
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 run pdb2gmx -failing to recognise the identifier NAG - is there an alternative identifier I can use? Thanks, David -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] extending npt step/generating output from crashed/fatal error-based quit session.
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 topol.tpr, is there a way to either output what I need for the production run from what I have or a set of commands that allow me to finish the crashed sim? Thanks, David -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] empty index group
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 is for linking separate options together not separate instances of the same option. Is there a way to achieve what I'm after? Thanks, David -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
