Hi,
You can just strip out any atoms that the topologies do not have in
common. For example, say that protein 1 is residues 1-270 and protein
2 is residues 1-273 (i.e. it has 3 extra residues, all other residues
the same):
parm top1.parm7
trajin traj1.nc parm top1.parm7
parm top2.parm7
trajin traj2.nc parm top2.parm7
strip :271-273 parmout combined.parm7
trajout combined.nc
You could then run the RMSF calc using combined.parm7 and combined.nc.
If the residues in common are not so straightforward, you will have to
do two rounds of 'strip'. For example say the residues in common are
residues 2-250 from protein 1 and 12-260 from protein 2:
# Strip protein 1
parm top1.parm7
trajin traj1.nc parm top1.parm7
strip !(:2-250) parmout combined.parm7
trajout combined.nc
run
# Strip protein 2 and append
clear trajin
parm top2.parm7
trajin traj2.nc parm top2.parm7
strip !(:12-260)
trajout combined.nc append
run
I highly recommend consulting the cpptraj manual on these commands so
you can understand what each keyword/command is doing.
Hope this helps,
-Dan
On Fri, May 17, 2019 at 1:29 AM Rinsha Chk <rinshachk.gmail.com> wrote:
>
> Thank you for the reply Bill.
> The atom orders are the same. But when I use the 'atomicfluct' command for
> RMSF calculation it ends up in an error like "Error: AtomicFluct not yet
> supported for mulitple topologies with different #s of atoms". if that
> is the case, then how one can determine the RMSF?
>
> On Thu, May 16, 2019 at 5:29 PM Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > Are the connectivities and mot importantly, the atom orders the same?
> > If so, the prmtop shouldn't matter, unless you are using mass-weighted
> > RMS and the topologies use different atom masses, I believe.
> >
> > Bill
> >
> > On 5/16/19 4:43 AM, Rinsha Chk wrote:
> > > Hello,
> > > I had combined trajectories with different topology file, in order to get
> > > rmsf of the combined trajectory which topology should I use?
> > > _______________________________________________
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> >
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>
>
> --
> Rinsha. C H
> Research Scholar
> Theoretical and Computational Chemistry Lab
> Department of Chemistry
> NIT Calicut
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Received on Fri May 17 2019 - 05:30:02 PDT
