Dear Jag,
why don't you just use this software that you've mentioned? It is
supposed to accept PDB files, so just convert your original trajectory
with cpptraj.
Kind Regards,
Szymon Żaczek
2018-01-14 18:06 GMT+01:00 Jag Silwal <jagsilwal.gmail.com>:
> 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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Received on Mon Jan 15 2018 - 03:30:02 PST
