[gmx-users] About pdb2gmx and cyclic peptides

[Ivan Gladich]

Dear all,
    I am trying to build a cyclic peptide of 12 aminoacids using pdb2gmx.
Searching on the web I found that is not very straightforward without 
editing the topology and the .gro file

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2012-September/074609.html

The problem is that I have thousand of structures and so I need to do it 
iteratively.
I am wondering if in the newer versions of gromacs the problem has been 
addressed and solved.

Thanks for any possible advice
Ivan

-- 
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Ivan Gladich, Ph.D.
Research Assistant
International School for Advanced Studies (SISSA)
Via Bonomea 265, I-34136, Trieste,
Italy

Room: 331
Tel: +390403787335
e-mail: igladich at sissa.it
web page: http://people.sissa.it/~igladich/