C Johnson wrote:
You've indicated in the topology that there are two peptides, but you've only
built a coordinate file that contains one. If you want to simulate two
peptides, you have to build a configuration that contains two peptides.
Are you saying that I cannot use the pdb file with a single molecule? I would
have to make a pdb file
with multiple molecules instead?
Precisely. A topology file cannot modify a coordinate file, and vice versa.
They are complementary.
-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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