Hi,
As far as I know, this should work. Could you send me (off-list) a
topology file and restart file (or alternatively a PDB file) so that I
can try and reproduce the behavior you are seeing and track down any
issues? Thanks.
-Dan
On Mon, Oct 15, 2012 at 2:19 AM, Vijay Manickam Achari
<vjrajamany.yahoo.com> wrote:
> Dear Daniel,
>
> Thanks for your reply.
>
> As you suggested I have made the angle to be zero (angle 0.0) and run the ptraj program (in amber 12) to get the intra-molecular hydrogen bonding (hydrogen bonding within the same residue). I checked the result of this calculation, which is in the form of table, looking for a line which should contain same residue numbers but unfortunately I could not find one. Means this command do not calculate the INTRA molecular hydrogen bonding.
>
> Just curious to know, is there any other way to calculate this INTRA molecular hydrogen bonding?
>
> Many thanks in advance.
>
> Regards
>
>
> Vijay Manickam Achari
> (Phd Student c/o Prof Rauzah Hashim)
> Chemistry Department,
> University of Malaya,
> Malaysia
> vjramana.gmail.com
>
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> To: Vijay Manickam Achari <vjrajamany.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
> Sent: Saturday, 6 October 2012, 1:43
> Subject: Re: [AMBER] calculating intramolecular hydrogen bonding
>
> Hi,
>
> On Fri, Oct 5, 2012 at 1:29 AM, Vijay Manickam Achari
> <vjrajamany.yahoo.com> wrote:
>> I found one thread in amber mailing list talking about this (http://archive.ambermd.org/201007/0679.html) but I am not so clear how the "angle turning off" (angle = -1.0) could give intramolecular hydrogen bonding values.
>
> You don't need to turn off the angle calculation, that just removes
> the angle criterion from hydrogen bond determination.
>
> You could also try the 'hbond' command in cpptraj which doesn't
> require you to specify donors/acceptors ahead of time.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Oct 17 2012 - 07:00:12 PDT
