Thank you all for your help.
I used the command that works:
distance ser_hid :57.906 :97.1568 out dist_ser_hid.agr
All the best,
Michael
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il
________________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Saturday, August 15, 2015 6:13 PM
To: AMBER Mailing List
Subject: Re: [AMBER] RMSD and average value of interatomic distance?
>From the Amber15 manual for the cpptraj command 'distance' (29.9.19):
distance [<name>] <mask1> <mask2> [out <filename>] [geom] [noimage] [type noe]
You will need to use Amber atom mask expressions for <mask1> and
<mask2>. Amber atom mask syntax is thoroughly explained in section
29.1.6 (Atom Mask Selection Syntax). For example, atom number 906 is
selected by ".906".
In my opinion it's definitely worth it to spend some time with the
manual and tutorials - this way you can get a better idea of what
functionality is available and how best to use it.
Hope this helps,
-Dan
On Sat, Aug 15, 2015 at 8:49 AM, Michael Shokhen
<michael.shokhen.biu.ac.il> wrote:
> Dear Jason and Adrian,
>
> Many thanks for your advices.
> I have send to amber list my replay on your emails
> but it seems that my second email didn't arrive.
> In short: I didn't succeed. Please find details below
> in a copy of my second email.
> What I need is your correction of my wrong command.
>
>
>>
>> I have read again the cpptraj tutorial you recommended.
>> I have defined topology and trajectory as well as strip
>> water and counter ions. Unfortunately, the command
>> for setting distance between two atoms is absent in the tutorial,
>> so I have constructed the following command:
>>
>>> distance ser_hid iat= 906,1568 out dist_ser_hid.agr
>> Error: distance: Requires 2 masks
>> Error: Could not initialize action [distance]
>>
>> As you see that was wrong because of the iat= 906,1568 parameter.
>> Please give me the correct command variant.
>>
>> Thank you,
>> Michael
>
>
>
> *****************************
> Michael Shokhen, PhD
> Associate Professor
> Department of Chemistry
> Bar Ilan University,
> Ramat Gan, 52900
> Israel
> email: shokhen.mail.biu.ac.il
>
> ________________________________________
> From: Adrian Roitberg <roitberg.ufl.edu>
> Sent: Saturday, August 15, 2015 5:15 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] RMSD and average value of interatomic distance?
>
> Michael
>
> http://ambermd.org/tutorials/analysis/tutorial0/#Processing_the_Trajectory
>
> under Specifying an Action
>
> it even tells you how to execute a
> help distance command !
>
> adrian
>
>
> On 8/15/15 10:12 AM, Michael Shokhen wrote:
>> Hi Jason,
>>
>> I have read again the cpptraj tutorial you recommended.
>> I have defined topology and trajectory as well as strip
>> water and counter ions. Unfortunately, the command
>> for setting distance between two atoms is absent in the tutorial,
>> so I have constructed the following command:
>>
>>> distance ser_hid iat= 906,1568 out dist_ser_hid.agr
>> Error: distance: Requires 2 masks
>> Error: Could not initialize action [distance]
>>
>> As you see that was wrong because of the iat= 906,1568 parameter.
>> Please give me the correct command variant.
>>
>> Thank you,
>> Michael
>>
>>
>>
>>
>>
>>
>> *****************************
>> Michael Shokhen, PhD
>> Associate Professor
>> Department of Chemistry
>> Bar Ilan University,
>> Ramat Gan, 52900
>> Israel
>> email: shokhen.mail.biu.ac.il
>>
>> ________________________________________
>> From: Jason Swails <jason.swails.gmail.com>
>> Sent: Saturday, August 15, 2015 3:45 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] RMSD and average value of interatomic distance?
>>
>> These sound like questions that the existing cpptraj tutorials go through
>> nicely:
>>
>> http://ambermd.org/tutorials/#analysis
>>
>> HTH,
>> Jason
>>
>> On Sat, Aug 15, 2015 at 3:30 AM, Michael Shokhen <michael.shokhen.biu.ac.il>
>> wrote:
>>
>>> Dear Amber list members,
>>>
>>> I need to estimate RMSD and average value
>>> of interatomic distance over MD trajectory
>>> for two atoms:
>>>
>>> The first atom
>>> atom number in protein: 1568
>>> atom type: NE2
>>> Residue # 92, HID
>>>
>>> The second atom
>>> atom number in protein: 906
>>> atom type: OG
>>> Residue # 57, Ser
>>>
>>> How to write command for cpptraj?
>>>
>>> Thank you,
>>> Michael
>>>
>>>
>>>
>>>
>>> *****************************
>>> Michael Shokhen, PhD
>>> Associate Professor
>>> Department of Chemistry
>>> Bar Ilan University,
>>> Ramat Gan, 52900
>>> Israel
>>> email: shokhen.mail.biu.ac.il<
>>> https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> Dr. Adrian E. Roitberg
> Professor.
> Department of Chemistry
> University of Florida
> roitberg.ufl.edu
> 352-392-6972
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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 Sat Aug 15 2015 - 09:00:04 PDT
