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

[Tamir Dingjan]

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
appropriate.

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

Kind regards,
Tamir




-- 

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

www.pharm.monash.edu.au


<http://www.linkedin.com/pub/tamir-dingjan/50/282/82b>