Dear Jesmita,
> I have docked graphene oxide to human
> lysozyme protein. I want to run md simulation, but can not able
> generate the parameter file using antechamber as its very large
> sturcture.
I think the main problem is the algorithm - not the size of your molecule:
Antechamber (at least former versions; no idea about the last one)
does not deal with molecules with many cycles; so you end up with the
type of error your reported "the actual number of rings (7134) exceeds
the defaut ring size"; so you have to modify the source code (I guess)
to increase the right parameter and recompile, ... and then the same
error will show up for a larger molecular system... This is a never
ending problem or you end up with a huge untractable parameter in the
source code...
You could use PyRED at R.E.D. Server, where the algorithm used for
chemical equivalencing and atom typing does work for molecules with
many cycles such as fullerenes, CNT and functionalized CNT. Then at
R.E.D. Server Dev. you will end up with a limit related to the size of
the your molecule (so far 225 atoms).
See
http://upjv.q4md-forcefieldtools.org/REDServer-Development/faq.php#17
Just send an email to contact_at_q4md-forcefieldtools.org, and request
to postpone this limit; obviously you have to reasonable ;-)
Do not forget to add the hydrogen atoms in your input PDB file...
I hope this helps.
regards, Francois
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Fri Feb 26 2016 - 01:30:05 PST
