Can you provide some more details about the system? What are residues
1-22 and residues 23-1030? A non-native contact is simply one that
wasn't present in the reference frame (in this case the first frame),
so if your system moves into a configuration that is very different
from the reference you can have a high number of non-native contacts..
1075 does seem very high though - have you visually inspected your
trajectory for artifacts? At this point without seeing more of the
cpptraj output, the output data, or the trajectory itself I can only
speculate.
-Dan
On Mon, Mar 21, 2016 at 6:57 PM, Krantzman, Kristin D
<KrantzmanK.cofc.edu> wrote:
> Hi Dan,
> The version is AmberTools 15.
> Kristin
> ________________________________________
> From: Daniel Roe [daniel.r.roe.gmail.com]
> Sent: Monday, March 21, 2016 8:53 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] strange output with nativecontacts command
>
> Hi,
>
> What version of cpptraj are you using?
>
> -Dan
>
> On Mon, Mar 21, 2016 at 6:22 PM, Krantzman, Kristin D
> <KrantzmanK.cofc.edu> wrote:
>> Greetings,
>> I am using the nativecontacts command to determine the number of contacts between a protein and a surface:
>> nativecontacts :1-22 :23-1030 distance 3.0 out contacts.dat
>> Residues 1-22 have a total of 202 atoms and the initial number of native contacts is 21.
>> The number of nonnative contacts spikes to numbers as large as 1075 in certain frames. Is this a bug? I am wondering why the number of contacts becomes so large. This is physically unrealistic
>> Thank you in advance.
>> Best, Kristin Krantzman
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>
>
> --
> -------------------------
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Mar 21 2016 - 19:00:03 PDT
