Dear Juan,
So how it looks
distance R1-R2 R3 .CA out xyz.dat
Does R1-R2 will define the centre between these two residues?
On Tue, Jun 9, 2015 at 10:57 AM, Juan Eiros Zamora <
j.eiros-zamora14.imperial.ac.uk> wrote:
> My bad,
>
> I just saw that you were refering to the center of mass
>
> So ignore the 'geom' keyword because that's the default option for cpptraj
>
> On 09/06/15 09:55, Juan Eiros Zamora wrote:
> > Hi,
> >
> > You can specify the 'geom' option in the distance command in cpptraj. I
> > think the following command:
> >
> > distance R1-R2 R3 out filename.dat geom
> >
> >
> > should work. You can see the info in section 29.9.19 of the manual
> >
> > Cheers
> > Juan
> >
> > On 09/06/15 09:33, Soumendranath Bhakat wrote:
> >> Dear Amberists,
> >>
> >> I have three residues R1, R2 and R3. I wish to calculate the centre of
> mass
> >> between R1 and R2 and then calculate distance of R3 from the centre of
> >> mass.
> >>
> >> Can anyone suggest how to do this operation with CPPTRAJ?
> >>
> >> Thanks in advance,
> >>
> >> /SB
> >>
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>
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--
Thanks & Regards;
Soumendranath Bhakat
Research Assistant, Division of Biophysical Chemistry, CMPS, Lund
University, Sweden
Homepgae: https://cbiores.wordpress.com/
ResearchGate: https://www.researchgate.net/profile/Soumendranath_Bhakat2
Google Scholar: http://scholar.google.com/citations?user=Q1_nDMcAAAAJ&hl=en
Past: Molecular Modelling and Drug Design Research Group
Discipline of Pharmaceutical Sciences
UKZN, Westville
Weblink: http://soliman.ukzn.ac.za/Home.aspx
and Department of Pharmaceutical Sciences
Birla Institute of Technology, Mesra, India
in.linkedin.com/pub/soumendranath-bhakat/15/79b/b9/
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Received on Tue Jun 09 2015 - 02:30:02 PDT
