Thanks Dan for your quick and kind support! Yes, I think we agree that
for a "simple" and common task like mine, it would be great to have a
single intuitive command.
All the best and thanks again,
Jan-Philip
On 02.05.2013 16:22, Daniel Roe wrote:
> Hi,
>
> The only way I can currently think of to specifically get h-bonds
> between only two molecules is with two hbond commands, e.g. (here
> receptor mask is :REC and ligand mask is :LIG):
>
> hbond REC-LIG donormask :REC acceptormask :LIG out Nhbond.agr avgout REC-LIG.dat
> hbond LIG-REC donormask :LIG acceptormask :REC out Nhbond.agr avgout LIG-REC.dat
>
> You can then construct the total h-bonds observed from Nhbond.agr,
> REC-LIG.dat, and LIG-REC.dat.
>
> The issue is that the code currently does not have a simple way to
> exclude hydrogen bonds based on what molecule they are in (except for
> solvent of course but that's a special case and certainly not
> applicable here). I think what the h-bond command needs is a keyword
> that will specify tracking of intra-molecular h-bonds only. It's added
> to my to-do list.
>
> Hope this helped,
>
> -Dan
>
> On Thu, May 2, 2013 at 6:30 AM, Jan-Philip Gehrcke
> <jgehrcke.googlemail.com> wrote:
>> Hallo (especially to Dan),
>>
>> I am trying to become familiar with cpptraj's hbond command. For a
>> trajectory containing receptor and ligand molecules I am trying to
>> collect information about all hydrogen bonds formed between receptor and
>> ligand throughout the trajectory. Hence, my requirements:
>>
>> - The interest is only in inter-molecular hbonds, not in intra-molecular
>> ones.
>> - Both, ligand as well as receptor atoms may serve as donor as well as
>> acceptor.
>> - I only need to consider the standard acceptors F, O, N.
>>
>> From the documentation it is not clear to me how to construct a
>> corresponding hbond command.
>>
>> Example: Given two masks of residue IDs, e.g. :1-100 for the receptor
>> and :101-110 for the ligand, I want hydrogen bonding information printed
>> to the avgout file (according to the requirements stated above). How
>> would I do that?
>>
>> Thanks for your help,
>>
>> Jan-Philip
>>
>>
>>
>>
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>
>
>
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Received on Thu May 02 2013 - 08:30:02 PDT
