Quoting Lan Hua <lan.hua.gmail.com>:
> 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.
Dear Lan Hua,
I ask you to excuse me for not responding... I will contact you this week-end.
You can indeed use R.E.D. or even R.E.D. Server to generate ESP or
RESP charges embedded in FF libraries for Acetyl-CoA & derivatives.
regards, Francois
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Received on Fri Jan 22 2010 - 12:30:02 PST
