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
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Received on Sat Aug 15 2015 - 08:00:04 PDT
