ZHAO Lina wrote:
Hi,
after added ions, I got a solv_ions.gro.
I use trjconv
to produce the solv_ions.pdb
when I view it in pymol.
I showed sequence,
it like
1 2 3 4 6
ODOAOEOROHODOGOOYE
But the solv_ions.pdb looks pretty regular.
my problem is that,
how could I choose the protein parts.
I tried the select protein, resi 1-48
some waters are inclusive.
Do you have a very large system? If so, PDB format can only handle a fixed
number of digits in the residue and atom numbering fields, so the numbering of
your waters restarts from zero. Such is the limitation when dealing with .pdb
files.
If you just need to make selections in PyMOL, strip the water out of the file
first.
-Justin
Thanks for any suggestion.
lina
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
