>> I won't commit to an actual answer of your question since I don't know
how you modified the file. The general answer is "no, because of extra
lines like TER cards", but if you've removed them then it's possible you're
correct.
grep ATOM is your friend and it works! or any other keyword you want.
>> This is an example of a question where investigating yourself is far
better than asking on a list
My concern was just how cpptraj internal numbering works. I did not ask
e.g. for an atom number 1024 should be line 1024. And also when you say is
atom 105,501 on line 105,501, for a moment forget about line number, then
how you are confident that atom number you know is indeed 105,501. I mean
from where did you get this atom number (probably CIF file as you said or
topology)? I just asked is this line number (specially for the case when N
> 99999) should be same as internal cpptraj numbering? I think the answer
is yes.I was asking this simply.
best
On Wed, Jul 23, 2014 at 5:03 PM, Jason Swails <jason.swails.gmail.com>
wrote:
>
> On Jul 23, 2014, at 8:23 AM, newamber list <newamberlist.gmail.com> wrote:
>
> > Dear Jason and Daniel,
> >
> > Thanks here are my replies:
> >
> >>> The line number trick won't work because molecules are separated by TER
> > cards
> > yes I removed all that extra lines, Just ATOM info is there
> >
> > Actually I want to do analysis on some atom whose coordinates (read from
> > PDB) fall in some my selection criteria. This atom number in PDB is more
> > than 99999 so if ATOM number is taken from PDB it will be actually wrong.
> > So using line number should correspond to correct atom number. So my
> > question: Is this line number (= atom number) should be the same atom
> > number which cpptraj uses internal numbering?
>
> We have already described how cpptraj numbers its atoms. It goes from 1
> to N. I won't commit to an actual answer of your question since I don't
> know how you modified the file. The general answer is "no, because of
> extra lines like TER cards", but if you've removed them then it's possible
> you're correct.
>
> It's far easier to just check yourself. Go to a handful of different
> lines in your file. For example, is atom 1024 on line 1024? Is atom
> 100,001 on line 100,001? This should be easy to determine since the
> numbering restarts on the line above. Is atom 105,501 on line 105,501? If
> the answer to all of these questions is "yes", then you can be confident
> that line numbers correspond to atom numbers. This is an example of a
> question where investigating yourself is far better than asking on a list.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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>
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Received on Wed Jul 23 2014 - 10:00:02 PDT
