[gmx-users] end capping

XAvier Periole x.periole at rug.nl
Sat Dec 7 17:27:06 CET 2013

You can choose different termini by setting the option term (-term) to pdb2gmx. 

The ff gromos 53a6 has a strong tendency to destabilize alpha helices and favors sheets. If you like to stick to gromos ff you need to switch to the 54a7 more recent version to which a rectification of this bias has been attempt. 

> On Dec 7, 2013, at 14:11, Shine A <shine.a at iisertvm.ac.in> wrote:
> Sir,
>        I am using MD to study the folding of peptides. Now I want to
> modify N terminal of the peptide with acetyl group and C terminus with
> amide group.How Can I do this? What are the changes I should made in
> various files? Gromos96 53a6 is using for simulation.
>                     Thank in advance
> -- 
> 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-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list