Hi Francois,
Thank you for your reply. We don't have any account on R.E.D. Since
only PI can register, I prefer to find the force field parameters for
Acetyl-CoA myself first. So I appreciate very much if you could show me
where to get these force field parameters when you get time. Thanks again.
Best,
Lan
On Fri, Jan 22, 2010 at 12:10 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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 - 13:00:02 PST
