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. >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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