Thank you, Dan, It worked.
Thanks a lot to you both...
On Fri, May 17, 2019 at 5:53 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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?
> > > > _______________________________________________
> > > > 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
> > >
> >
> >
> > --
> > Rinsha. C H
> > Research Scholar
> > Theoretical and Computational Chemistry Lab
> > Department of Chemistry
> > NIT Calicut
> > _______________________________________________
> > 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
>
--
Rinsha. C H
Research Scholar
Theoretical and Computational Chemistry Lab
Department of Chemistry
NIT Calicut
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun May 19 2019 - 21:30:01 PDT
