swati shah wrote:
Dear Gromacs Users,
Can we perform gromacs analysis on any two molecules like peptide+
peptide or DNA+ RNA? and what might be the setup and process if we
wanted to sim a peptide + a peptide with a small molecule causing a PTM
event. If we can do so then do we have any options to select two
peptides with one or more having PTM via small molecule. What might be
the sequence of events in this use case.
Any suggestion??
Your series of questions is extremely broad, especially the use of the phrase
"Gromacs analysis." What do you mean? Do you wish to study the effect of a
post-translational modification (PTM) on peptide aggregation? Or binding
studies of peptides and nucleic acid?
In theory, you can set up just about anything you want. Gromacs is versatile
like that. If you're looking at covalent PTM events, then no, you can't do it
with classical mechanics, which does not allow for bond breaking or forming. If
you want to study the effects of small molecules on aggregation, that's also
possible. The conditions depend entirely upon what's known about such a system.
If you ask a more focused, specific question, you're more likely to get a real
answer.
-Justin
Thanks,
SWati
--
========================================
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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