# Re: [AMBER] cpptraj RMSD calculation with mismatch residue numbers

From: anu chandra <anu80125.gmail.com>
Date: Fri, 18 Nov 2016 13:12:32 +0000

Hi,

Thanks for the information. Here, how will I specify two different residue
range for input trajectories . For example,

parm ABdomain.top [AB]
parm Bdomain.top [B]

trajin 1md.nc parm [AB] #Here, B domain residue numbering is from 101 -
200
trajin 2md.nc parm [AB] #Here, B domain residue numbering is from 101 -
200
trajin 1md.nc parm [B] #Here, B domain residue numbering is from 1-100
trajin 2md.nc parm [B] #Here, B domain residue numbering is from 1-100

reference ABdomain.crd parm [AB]

#command to calculate the RMSD of B domain ( ie. residue 101-200 from first
two set of trajectories and 1-100 from second two set of trajectories)

Many thanks

Anu

On Wed, Nov 16, 2016 at 11:26 PM, Nhai <nhai.qn.gmail.com> wrote:

> You can specify reference mask
>
> Check this link for example
> https://github.com/Amber-MD/cpptraj/blob/1a6ceaa7703c9d694c6b0717cf2c2c
> 8f05353469/test/Test_General/RunTest.sh#L38-L39
>
> Hai
>
> > On Nov 16, 2016, at 6:02 PM, anu chandra <anu80125.gmail.com> wrote:
> >
> > Dear Amber users,
> >
> > I am working with a two domain protein, A domain (residue 1 -100) and B
> > domain (101-200). After 100 ns simulation of two domains together, I
> > removed the A domain and continued the simulation for another 100 ns (
> For
> > this purpose, I basically generated a new system with conformation of B
> > domain obtained after 100 ns simulation of AB domain together). In the
> > second set of simulation, since the A domain was removed the residue
> > numbering for B domain has changed to 1 - 100.
> >
> > Now, I am trying to calculate the RMSD of B domain over whole 200 ns
> > simulation time (100 + 100) with reference to the starting conformation
> of
> > B domain (ie. at t = 0). Since there is mismatch of residue numbering in
> B
> > domain, I just looking for a way to calculate RMSD with cpptraj. A
> possible
> > input file should have following workflow,
> >
> > parm ABdomain.top [AB]
> > parm Bdomain.top [B]
> >
> > trajin 1md.nc parm [AB]
> > trajin 2md.nc parm [AB]
> > trajin 1md.nc parm [B]
> > trajin 2md.nc parm [B]
> >
> > reference ABdomain.crd parm [AB]
> >
> > #command to calculate the RMSD of B domain ( ie. residue 101-200 from
> first
> > two set of trajectories and 1-100 from second two set of trajectories)
> >
> >
> >
> >
> > Any help would be highly appreciated
> >
> > Anu
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> > AMBER.ambermd.org
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Received on Fri Nov 18 2016 - 05:30:03 PST
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