[gmx-users] Apply secondary structure restraints only on part of the peptide while coarse graining
tsjerkw at gmail.com
Wed Nov 12 21:26:51 CET 2014
You can supply a secondary structure string with the option -ss. That may
also be provided as a file. you can also just modify the residues you need
to have different in the dssp output. Only the actual classification string
Hope it helps,
On Nov 12, 2014 4:00 PM, "shivangi nangia" <shivangi.nangia at gmail.com>
> Hello Dear GMX users,
> I want to apply secondary structure constraints only on a part of my
> peptide while coarse graining (martinize.py), which contains a helical part
> and the rest of the structure is disordered.
> If I supply a .dssp file only of part of the peptide, I only get the first
> coarse grained part of the peptide back.
> Is there a way around this?
> Kindly suggest.
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * 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