[gmx-users] a question on g_hbond

Justin Lemkul jalemkul at vt.edu
Sun Nov 4 13:56:16 CET 2012

On 11/4/12 6:02 AM, David van der Spoel wrote:
> 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?

Use the -hbn and -hbm options.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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