[gmx-users] g-hbond and N acceptors

[Michel Cuendet]

David,

Thanks for your reply.

> NH2 groups that are not aromatic (amines) 
>one accept Hbonds of course. However there is not so much chemical 
>knowledge in the program, and to make matters worse, you can not select 
>acceptors or donors separately.
>
Of course amine groups with a lone electron pair can in principle accept 
H-bonds. But in the case of proteins, no such groups are found  (except 
on a deprotonated Lys). Peptide groups in the backbone as well as 
carboxyamide groups on Asn and Gln have hybrid orbitals which makes 
their structure planar and prevents to accept H-bonds. In proteins at 
reasonable pH, only deprotonated aromatic nitrogens on His should be 
considered acceptors. The GROMOS and HBPLUS manuals agree on this. In 
HBPLUS there is an option to accept other nitrogens as acceptors (see 
below) but only in cases where the protonation of His and orientation of 
Asn and Gln are not determined. These nitrogens are not considered 
acceptors by themselves.

I would like to hack a correction for this in the code.  I guess I would 
have to simply change line 400 of gmx_hbond.c (3.3.1) with something like :

(*top->atoms.atomtype[i])[0] == 'NR5')

Does this look right ? What is the difference between atomtype and 
atomtypeB ?

Cheers,
Michel

========================================================================
FROM THE HBPLUS MANUAL

Acceptors :

1.  O (ie Main Chain COs of recognised amino - not imino - acid residues)

2.  CYH SG, CSS SG, ASP OD1, ASP OD2, GLU OE1, GLU OE2, HIS ND1, MET SD,
    ASN OD1, GLN OE1, SER OG, THR OG1, TYR OH 

3.  Recognised acceptors of non-standard recognised molecules

4.  Oxygen atoms in HETATM molecules (including waters)

Atoms that may act as both donors and acceptors under the -X or -x options :

1.  HIS CD2, HIS CE1, ASN OD1, ASN ND2, GLN OE1, GLN NE2

-x      Exchange the side-chains of Histidine, Glutamine and Asparagnine.
These side-chains are difficult to resolve crystallographically with
certainty, which is why there is the option of adding potential hydrogen
bonds that would be formed if HIS CD2 was actually ND1, HIS CE1 was NE2 and
the nitrogens and oxygens of the ASN / GLN amide groups were actually the
other way round.  (Default is not to do this.)
========================================================================





-- 

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Michel Cuendet, Ph.D
Molecular Modeling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
www.isb-sib.ch/groups/Molecular_Modeling.htm
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