Re: [AMBER] peptideligandParameters

From: Jason Swails <>
Date: Fri, 24 Oct 2014 08:48:15 -0400

On Thu, Oct 23, 2014 at 4:58 AM, zayan alhalabi <>

> I would like to ask you about the parameters for
> ​​
> peptide ,my peptide has a small modification
> :3,3-dimethyle-succinyle-lysine peptide and also it has benzoyl chemical
> group in the c- terminal ... how can I generate the
> ​​
> ​​
> ​​
> parameters for this peptide befor doing MD with the protein.

​This is a challenging task that may take some time to complete. Hopefully
the first "advanced" tutorial can help provide pointers about what you have
to do: While the task in
that tutorial is similar to what you are trying here, it is a little bit

> ​​
> and when I tried to generate parameters in antechamber and then x-leap ,
> the x-leap always give me wrong charges and missing parameters for many
> atoms .

​​​This statement is too vague to be of any use to people trying to help.
In order to even try to help you with your problem, we have to be able to
understand _exactly_ what it is. Since there are so many ways for
something "to go wrong" in Amber, there is no way to plausibly guess what
happened from vague information. Be specific. Be concise.

Good luck,
​​P.S. There is a very good reference describing what it means to ask
"good" technical questions to these types of forums, and much of it will be
applicable to forums you encounter in this field (​
Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 24 2014 - 06:00:05 PDT
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