Hi Dan,
Yes, the trajectory has been subject to rms fitting before the nativecontacts command. Thank you for your help in diagnosing this problem. Best, Kristin
From: Daniel Roe [daniel.r.roe.gmail.com]
Sent: Tuesday, March 22, 2016 3:38 PM
To: AMBER Mailing List
Subject: Re: [AMBER] strange output with nativecontacts command
On Tue, Mar 22, 2016 at 12:58 PM, Krantzman, Kristin D
<KrantzmanK.cofc.edu> wrote:
> Hi Dan,
> Thank you for your suggestions. When I use the noimage option with cpptraj, the number of contacts decreases.
Does the value decrease to something you consider "reasonable"? If so
I would suspect some prior RMS fitting of the trajectory. Do you know
if the input trajectory has been subject to an RMS best-fit
previously?
-Dan
> I am not certain how to obtain a list of the atoms that are involved in nonnative contacts with cpptraj. When I use the byres and resout commands, I only get the residues involved in native contacts. Is there a way to obtain a list of the residues and atoms involved in nonnative contacts?
> Thank you.
> Best, Kristin
> ________________________________________
> From: Daniel Roe [daniel.r.roe.gmail.com]
> Sent: Monday, March 21, 2016 9:52 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] strange output with nativecontacts command
>
> 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
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=PrC73kDcMgSH8y1TTcMFzMhVou6rz46HNOhMpXsyB5A&s=0kZ-uDCy4keG9ifqO12Ouw1ThrbkHun7oHkZjuHD2w8&e=
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__home.chpc.utah.edu_-7Echeatham_&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=PrC73kDcMgSH8y1TTcMFzMhVou6rz46HNOhMpXsyB5A&s=LvHyIBooGueAg3wbH-OwU2iL4oPX0c1Z06y0HKJ9dSc&e=
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=PrC73kDcMgSH8y1TTcMFzMhVou6rz46HNOhMpXsyB5A&s=0kZ-uDCy4keG9ifqO12Ouw1ThrbkHun7oHkZjuHD2w8&e=
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=EQXrCdVudxS4LsiBLqtwR3WN6NWQ8gOE6ZRBabsPOO8&s=wlVFprgudNmN9dJ3CKhWnuDPj1He4W2aiOM3rQ2l16o&e=
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> https://urldefense.proofpoint.com/v2/url?u=http-3A__home.chpc.utah.edu_-7Echeatham_&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=EQXrCdVudxS4LsiBLqtwR3WN6NWQ8gOE6ZRBabsPOO8&s=uzb-A27epGBCs2iSPsCVjnYWSI1obmbhfgSbeyRoesU&e=
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=EQXrCdVudxS4LsiBLqtwR3WN6NWQ8gOE6ZRBabsPOO8&s=wlVFprgudNmN9dJ3CKhWnuDPj1He4W2aiOM3rQ2l16o&e=
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=ZektDTWhcHDg_8pZ6oapobOSRKZTkEUpB_z4_X0FCts&s=FfKVyk5QasOsfRTUdPPvSo8tBAiG5TAb7-vnwbN529o&e=
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
https://urldefense.proofpoint.com/v2/url?u=http-3A__home.chpc.utah.edu_-7Echeatham_&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=ZektDTWhcHDg_8pZ6oapobOSRKZTkEUpB_z4_X0FCts&s=Psjdnj0yWwhiP2m15udfmuOqPCrDw3gIpYCt6blOkWM&e=
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=ZektDTWhcHDg_8pZ6oapobOSRKZTkEUpB_z4_X0FCts&s=FfKVyk5QasOsfRTUdPPvSo8tBAiG5TAb7-vnwbN529o&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 24 2016 - 11:00:04 PDT
