Justin A. Lemkul wrote:
maria goranovic wrote:
Thanks for the replies. I guess it is a very small bug. However, here
is another:
I have a 2-protein complex in water. The first protein residues
numbers are from residues 4 to 14, and the other from 5 to 9. In the
INPUT .gro file to grompp, I have a continuous numbering of residues
from 4 to 19 (4 to 14+5). However, after an energy minimization,
gromacs writes out a .gro file which preserves the original numbering
(4 to 14 and 5 to 9) instead of a numbering from 4 to 19. Why does it
do that? I can see the problem with such a numbering because I can
never unambiguously select "residue number 6" if I want to make an
index file. How does one go about fixing this?
I made the original input .gro file by using : editconf -f in.gro -o
out.gro -resnr 4
In the topology file, I read in protein_A.itp and protein_B.itp which
start from the original pdb residue number (4 and 5 respectively for
the two chains)
This is expected behavior and arises from pdb2gmx. The default is
pdb2gmx -norenum, preserving the original residue numbering. The
feature was implemented to make selections less ambiguous in the case of
missing residues (i.e. termini). You can get continuous numbering, if
you wish, by recreating the topology with pdb2gmx -renum.
In addition, you can always renumber any coordinate file using genconf -renumber
for the purpose of creating index groups.
-Justin
--
========================================
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
========================================
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