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?
Thanks
On Wed, Jul 23, 2014 at 3:12 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> It's not clear to me what you mean by 'feed some atom number to cpptraj'.
> The atom and residue numbers do indeed wrap back to 1 due to the fixed
> width of the fields in the PDB format, but cpptraj uses internal numbering
> when reading in PDB files, so there shouldn't be a problem. I may be able
> to provide more specific advice if you describe in detail exactly what you
> are trying to do and whether you are getting an error or not.
>
> -Dan
>
>
> On Tue, Jul 22, 2014 at 6:02 PM, newamber list <newamberlist.gmail.com>
> wrote:
>
> > Hi All
> >
> > I have a pdb file obtained from cpptraj. One common problem with pdb is
> > that resid or atom number restarts after 99999. So am just wondering
> would
> > line number be a good way of using atom number which I want should be
> same
> > as identified by cpptraj. I want to feed some atom number to cpptraj.
> >
> > Thanks
> > JIom
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> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
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Received on Wed Jul 23 2014 - 08:30:02 PDT
