[gmx-users] analysing ndx file of g_hbond

[Yang Ye]

Erik Marklund wrote:
> On Wed, 2006-06-28 at 22:37 +0800, Yang Ye wrote:
>   
>> Erik Marklund wrote:
>>     
>>> On Wed, 2006-06-28 at 04:29 -0700, raja wrote:
>>>   
>>>       
>>>> Dear all,
>>>>
>>>> The index file produced by g_hbond listing many rows of hbonds making
>>>> atoms combination. Is there a way to get the corresponding residue and
>>>> atom name for those numbers by any of the gromacs program or if anyone
>>>> having the script to do that, kindly pass it on to me. My primary
>>>> objective is to know how many hbond listed in index file are belong to
>>>> main chain atoms.
>>>>
>>>>     
>>>>         
>>> How about using make_ndx? Try the following:
>>>  X & Y
>>>   
>>>       
>> X | Y
>>
>> I was making the same mistake and still ask why I couldn't get it.
>>     
> I'm pretty sure it's supposed to be:
>
>  X & Y
>
> since you don't want to merge the main chain and the hbonds (union of X
> and Y = X | Y). Rather, you need to find the intersection of X and Y (=
> X & Y). Or haven't I understood your problem correctly?
>
> /Erik Marklund
>
>   
sorry. that's my misunderstanding.

>>>  q
>>> X being the index group containing the h-bonds and Y being the main
>>> chain index group. You will probably have to merge the g_hbond index
>>> file with an index file of your system first.
>>>
>>> Atom names and residues is slightly more problematic. I recommend using
>>> awk within a cshell (any shell would do) script to extract such
>>> information from a .gro-file of your system. Just loop through the
>>> g_hbond index file and have awk print atom names, residues, or whatever.
>>>
>>> Note that the ndx-file from h_bond is NOT merged (if I remember this
>>> correctly), so a-d-pairs are likely to show up several times in your
>>> index file. Depending on how you choose to use the index file, this
>>> could cause problems. This bug, along with a few other oddities, was
>>> fixed in the latest cvs version of g_hbond.
>>>
>>> /Erik Marklund
>>>
>>>   
>>>       
>>>> With thanks!
>>>> B.Nataraj
>>>> -- 
>>>>   raja
>>>>   raja_28 at fastmail.us
>>>>
>>>>     
>>>>         
>>
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>