Qian Wang wrote:
Hi,
I want to simulate two seperate peptids in one box. However, when I use
pdb2gmx to build the top file of this system, I found that gromacs
thought there is only one peptide because it added bond, angle and other
energy terms between the termius of these two peptides. Is there any way
to prevent this problem, or I need to change the top file by hand?
Thanks a lot.
When pdb2gmx processes an input coordinate file, it will assume the amino acid
sequence is one continuous protein unless you have either TER delimiters between
the chains or the chain ID (A, B, C...) changes. Then apply the appropriate
option to pdb2gmx -chainsep.
-Justin
Sincerely,
Qian
--
========================================
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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