Hi,
I'm not sure how HBPLUS defines a hydrophobic contact, but you could
potentially use the 'nativecontacts' command in cpptraj to track
contacts between non-polar atoms.
-Dan
On Sun, Jan 14, 2018 at 12:06 PM, Jag Silwal <jagsilwal.gmail.com> wrote:
> 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.
>
> http://www.tandfonline.com/doi/abs/10.1080/07391102.2012.732345
>
> Thank you,
>
> Sincerely,
> Jag
>
> On Sun, Jan 14, 2018 at 8:48 AM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> 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,
>> amber.ambermd.org, 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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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Tue Jan 16 2018 - 07:00:01 PST
