[gmx-users] Re: Hbonds - Res - Ligand

[Steven Neumann]

Hi Justin,

Do you have any clue of this problem? You are the last hope, please help :)

Steven

On Fri, Oct 28, 2011 at 2:45 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> With other residues is the same... and changes are bigger. Which trajectory
> in this case is reliable?
>
> My wsteps in trjconv involves:
>
>
> 1.      First make your molecules whole if you want them whole (system).
>
>
>
> 3.      Extract the first frame from the trajectory as reference for
> removing jumps if you want to remove jumps.
>
>
>
> 4.      Remove jumps if you want to have them removed using the first
> frame
>
>
>
> 5.      Center your system using some criterion. Doing so shifts the
> system, so don't use trjconv -pbc nojump after this step.
>
>
>
> 6.      Put everything in some box.
>
>
>
> 7.      Fit if desired and don't use any PBC related option afterwards.
>
>
>
>   On Fri, Oct 28, 2011 at 2:28 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:
>
>> Dear Gmx Users,
>>
>> I have compared average number of hbonds per time frame between my ligand
>> and protein:
>>
>> 1) Using trajectory obtained straight after simulations:
>>
>> g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num 91withLigandsHbond.xvg
>>
>> Avergage number of hbonds: 0.146
>>
>> 2) Using trajectory modified by trjconv according to the PBC workflow on
>> www.gromcacs.org :
>>
>> g_hbond -f md2final2.xtc -s md2.tpr -n SystemGRP.ndx -num
>> 91withLigandsHbond.xvg
>>
>> Avergage number of hbonds: 0.156
>>
>> Does anyone know why this value changed and I obtained slightly different
>> results?
>>
>> Thank you,
>>
>> Steven
>>
>
>
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