[gmx-users] g-hbond and N acceptors
David van der Spoel
spoel at xray.bmc.uu.se
Wed Nov 14 14:00:56 CET 2007
Michel Cuendet wrote:
> 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]) == 'NR5')
> Does this look right ? What is the difference between atomtype and
> atomtypeB ?
No, this is GROMOS specific. I would in that case prefer a solution like
that from HBPLUS you are describing, where there is an (optional) list
of atom names that are allowed. Problem is, that this is difficult to
make general, but putting all possible atom names for proteins and
DNA/RNA in there should be a good start.
The protonation state remains an issue though. We do quite a bit of
vacuum simulations and there one might have deprotonated N-terminal, Lys
and Arg, as well as protonated Asp, Glu and even Gln. Deprotonated
N-term and Lys side chain given an NH2 moiety which can accept. This
means it is not good enough to check atom names. Atomtypes are force
field dependent however, and therefore not suitable.
One could have an auto-generated list (like index files for proteins)
with the possibility of overriding this with an index file. Would that
be a good solution?
> 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.)
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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