[gmx-users] Residue representation

Steven Neumann s.neumann08 at gmail.com
Thu Jan 19 15:52:26 CET 2012

Dear Gmx Users,

I am simulating (Charmm27 ff) my protein in presence of a tube (made of
atoms). This tube is a representation of a surface of protein. I want to do
an approximation of residues on the surface. I divided amino acids and
represent them as:
- positively charged - I used Na+
[ SOD ]

[ atoms ]

SOD SOD 1.00 0

-negatively charged - I used CL-

[ CLA ]

[ atoms ]

CLA CLA -1.00 0

- hydrophilic - I took Oxygen from Tyrosine OH group

[ TYR ]

[ atoms ]

OH OH1 -0.54 13

- hydrophobic - I want to take Carbon atom - but I have no clue from which
group - I guess somethin positive? Or random Carbon from hydrophobic amino

Please, let me know your opinion for such representation. Would you suggest
representing charged amino acids by atoms taken from charged amino acids
(e.g. N from Arg?)

Do you think its a good approximation?

Thank you

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