Hi Amber users,
I want to run explicit MD simulations using Amber for a protein
complex system in which Acetyl-CoA (
http://en.wikipedia.org/wiki/Acetyl-CoA)
is the cofactor. So I need partial charges and force field parameters for
this molecule. I tried to use the antechamber module, but somehow I couldn't
get the partial charge. I searched amber mailing archives and found one
post which seems helpful,
http://archive.ambermd.org/200812/0328.html.
However, I couldn't find something related to Acetyl-CoA in the "List
projects" on the webpage of REDDB (
http://q4md-forcefieldtools.org/REDDB/index.php). I am wondering where I
can get the partial charge and parameters (ff03; Duan et al. version) for
Acetyl-CoA. Do I have to register to be a user at R.E.D to generate that?
If someone could share with me the partial charges and parameter for
Acetyl-CoA, I will highly appreciate this help. Thank you in advance.
Lan Hua
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Received on Fri Jan 22 2010 - 09:30:04 PST
