Re: [AMBER] Fwd: Hydrophobic interaction VS time in protein interfaces

From: Jag Silwal <>
Date: Sun, 14 Jan 2018 12:06:44 -0500

Thank you for your reply.

I read the following article and the authors have mentioned that they have
used a program called HBPLUS for such calculations. I just wanted to see if
there was a way in Amber as well.

Thank you,


On Sun, Jan 14, 2018 at 8:48 AM, David A Case <>

> On Sat, Jan 13, 2018, Jag Silwal wrote:
> >
> > I sent the following questions last week and maybe it is a really trivial
> > and easy question that I didn't get any reply from anyone. Could you
> please
> > throw in any insights? I would apprecaite your help.
> The hydrophobic effect is collective, and the idea of counting the number
> of
> hydrophobic interactions is tricky. There is no obvious way to do it in
> Amber, which is probably why no one answered. Also, I couldn't get the
> link
> to work well, and it was not clear what sort of plot you are interested in.
> Perhaps the methods section of the paper you read will provide details
> about
> how the calculations were done, or you could contact the authors for
> details.
> Please continue to send amber-related questions to the mail reflector,
>, and not to me personally. That way, many people can
> see your question and try to help, and the answers can help others with
> similar questions.
> ....dac
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Received on Sun Jan 14 2018 - 09:30:02 PST
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