[gmx-users] Exclude from [defaults] fudge values

Tamir Dingjan tamir.dingjan at monash.edu
Thu Sep 11 06:45:18 CEST 2014

Hi all,

I am simulating a protein-carbohydrate complex using AMBER99SB-ILDN for
protein and Glycam-derived parameters for the carbohydrate. The latter are
provided as Amber formatted topology files, and once converted into Gromacs
format using Acpype, include a [defaults] section with the following values:

nbfunc: 1
comb-rule: 2
gen-pairs: yes
fudgeLJ: 0.5
fudgeQQ: 0.8333

I would like to apply these values to the carbohydrate, but not the
protein. I suspect that the non-bonded function type and combination rule
are appropriate for both given the formatting of
amber99sb-ildn.ff/ffnonbonded.itp, but I don't think the fudge values are

How can I prevent the protein atoms in my simulation from being treated
using these fudge values?

Kind regards,


Tamir Dingjan

PhD Candidate

Faculty of Pharmacy and Pharmaceutical Sciences

Monash University (Parkville Campus)
381 Royal Parade, Parkville
Victoria 3052, Australia

Tel: Int + 61 3 9903 9187

E-mail: Tamir.Dingjan at monash.edu



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