[gmx-users] defining impropers necessary?

gromacs query gromacsquery at gmail.com
Wed Jul 17 16:37:50 CEST 2013

Dear All,

I have some polymer having peptide bond and want to use OPLSaa. I was
following Justin's example for building polymers

I have few queries:

1) do I need to define improper for peptide in .rtp file to keep it planar?

2) Also can pdb2gmx write improper by itself (in out .top file) depending
upon bond information and atom types defined in rtp file? Then there will
be no need to define impropers in rtp

3) Also can I use + before atom name more than once in one residue
(fragmented polymer)

thanks and regards,

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