Thanks Dan and others..
I tried following script in cpptraj..
parm WT.prmtop
parm GFP.prmtop
parm MIC.prmtop
parm mCherry.prmtop
trajin WT.mdcrd
trajin GFP.mdcrd
trajin MIC.mdcrd
trajin mCherry.mdcrd
reference WT.mdcrd 1 parm WT.prmtop [wt]
reference GFP.mdcrd 1 parm GFP.prmtop [gfp]
reference MIC.mdcrd 1 parm MIC.prmtop [mic]
reference mCherry.mdcrd 1 parm mCherry.prmtop [mch]
rms WT ref [wt] :1-88.C,CA,N,O out rmsd.dat
rms GFP ref [gfp] :1-88.C,CA,N,O out rmsd.dat
rms MIC ref [mic] :1-88.C,CA,N,O out rmsd.dat
rms mCherry ref [mch] :258-345.C,CA,N,O out rmsd.dat
But, I am sure something is wrong.. Because at step 1, rmsd value is not
zero for each case:
#Frame WT GFP MIC
1 0.0000 0.7683 0.6705
In the log file, I found that all trajectories were read using single
"WT.prmtop" file:
INPUT TRAJECTORIES:
0: 'WT.mdcrd' is an AMBER trajectory, Parm WT.prmtop (Trunc. Oct. box)
(reading 100 of 50100)
1: 'GFP.mdcrd' is an AMBER trajectory, Parm WT.prmtop (reading 100 of
179366)
2: 'MIC.mdcrd' is an AMBER trajectory, Parm WT.prmtop (reading 100 of
71554)
3: 'mCherry.mdcrd' is an AMBER trajectory, Parm WT.prmtop (reading 100 of
185989)
Coordinate processing will occur on 400 frames.
On Fri, Jul 29, 2016 at 9:02 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> . Hirdesh:
>
> adding to Dan's comment about cpptraj's flexibility: use can design their
> own protocol with pytraj ( :D )
>
> # Python stuff
> import pytraj as pt
>
> all_rmsd = [ ]
>
> for (fn, parm_name) in [('A.mdcrd', 'A.parm'),
> ('B.mdcrd', 'B.parm'),
> ('C.mdcrd', 'C.parm')]:
>
> traj = pt.iterload(fn, top=parm_name)
> # ref=0: first frame
> # ref=-1: last frame
> # and so on.
> rmsd_data = pt.rmsd(traj, ref=0)
> all_rmsd.append(rmsd_data)
>
> Hai
>
> On Fri, Jul 29, 2016 at 11:36 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
> > On Fri, Jul 29, 2016 at 9:30 AM, Carlos Simmerling
> > <carlos.simmerling.gmail.com> wrote:
> > > my guess is that cpptraj is not set up to load an arbitrary number of
> > > prmtop files,
> >
> > Cpptraj can load as many topology files as memory will allow. Loading
> > multiple topology files was actually one of my primary motivations for
> > writing cpptraj in the first place :-)
> >
> > -Dan
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Department of Medicinal Chemistry
> > University of Utah
> > 30 South 2000 East, Room 307
> > Salt Lake City, UT 84112-5820
> > http://home.chpc.utah.edu/~cheatham/
> > (801) 587-9652
> > (801) 585-6208 (Fax)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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Received on Fri Jul 29 2016 - 13:00:03 PDT
