[gmx-users] Problem to create topology using Amber force fields for single zitterionic amino acids.

Qaisrani Muhammad Nawaz mqaisran at ictp.it
Fri Mar 10 19:07:36 CET 2017

Dear all,

I wanna simulate a system made up of non covalent bonded glutamine
residues in water using different force fields, one of them belongs to
amber family (amber99sb-aldn). Problem using amber force field is that I
am not able to generate topology for zwitterionic single glutamine
residues. GLN, CGLN , NGLN are not working for me to create topolgy for
zwitterionic terminal charges of  single amino acid.

error I am getting are

In the chosen force field there is no residue type for 'GLN' as a
standalone (starting & ending) residue

There is a dangling bond at at least one of the terminal ends .... etc

If I add residue by myself in .rtp file then I am not sure the correct
parameterization of the charges that I added.

Any suggestion for this problem will highly be appreciated.


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