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

[Qaisrani Muhammad Nawaz]

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.

Thanks
Nawaz