[gmx-users] a question on g_hbond

David van der Spoel spoel at xray.bmc.uu.se
Sun Nov 4 12:02:47 CET 2012

On 2012-11-04 06:52, Acoot Brett wrote:
> Dear All,
> I have a protein complex PDB composed of chain A and Chain B. I want to dtermine the hydrogen bonds between chain A and chain B.
> By g_hbond it request me to input the group twice. But both chain A and chain B belong to group "protein". In this situation how can I determine the hydrogen bond between chain A and B?
you should make your own index file. e.g. using make_ndx.
> And if I want to which donor and acceptor form a hydrogen bond, which option of the g_hbond command has this function?
> I am looking forward to getting your reply.
> Cheers,
> Acoot

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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