[gmx-users] g_hbond and fluor

Ran Friedman r.friedman at bioc.uzh.ch
Tue Oct 13 08:53:45 CEST 2009

David van der Spoel wrote:
> Alvaro Cortes wrote:
>> Hi all.
>> I'm new at the list so i don't know if something similar has been
>> discussed before.
>> I tried to search in the archives, but i can't find something similar.
>> I have a doubt about g_hbond and fluor acceptors. As i can see in the
>> code, no parsing of F atoms is done in search_acceptors function in
>> gmx_hbond.c, so i added "|| ((*top->atoms.atomname[n])[0] == 'F') ||"
>> between oxygen and nitrogen parsing. This results in an increase of
>> the number of hbonds reported by the program but i dont know if this
>> little change  is enough or even correct.
>> Someone can bring me light in this stuff?
> I think it should be correct. Obviously it would be good to be more
> flexible without the need for user programming. In some contexts one
> might want to look for C-H ... 0 bonds as well and even N-H ...
> Aromatic interactions.
A bit off topic from the fluor-related issue, but if you modify g_hbond,
maybe it makes sense to disable nitogen atoms from being acceptors per
default. I don't think having nitrogen acceptors is very common.
>> Thank you in advance.
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