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
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Received on Sat Aug 15 2015 - 07:30:04 PDT
