From: Majid Shahbabaei (
Date: Wed Oct 28 2015 - 22:03:38 CDT

Dear Ashar,

Many thanks for your great explanations....


*Majid *

On Mon, Oct 19, 2015 at 7:44 PM, Ashar Malik <> wrote:

> Like i said before, I assumed you would be using some form of conventional
> naming.
> The one that I suggested was the simplest way.
> Since that doesn't work you can try experimenting --- you are just missing
> the "selection", the only person who knows your system is you, so you will
> have to do this on your own.
> What I can say is that --
> you can select based on many keywords.
> When you open the graphical representations window -- under the selected
> atoms box there are some tabs.
> press selections
> Underneath it are single words and keywords.
> UNKO means that your system doesn't adhere to conventional naming so you
> can see by selecting options in the keywords column - what values from your
> system are returned.
> as to your comment - just shows carbon atoms
> that is because your CNT has carbons which are defined by the keyword
> "name" value "C". You can open up the structure file/original PDB and see
> how stuff is labelled. e.g. resid and segid are also keywords and you can
> obtain values of it from your pdb and use these in your selection
> e.g.
> name C or segid "what you find" and type O
> if even that doesn't work for you - the method after that would be to use
> index which is how atoms are labelled in your structure file. anyway -- you
> will have to experiment with this --- from my understanding you should not
> have been able to fill up the xx entry -- since your label just showed you
> UNKO:O --- which means that there are more than 1 particles having a resid
> eitherway -- you will have to experiemtn with the selection keywords
> untill they work for you ....
> good luck ...
> if it doesn't work - send me the PDB/PSF -- and I will work out the
> selection for you ...
> Please do not send the trajectory just the PDB and PSF -- which you used
> to run your simulation.
> Best,
> /A