Thanks Daniel..
I
got
one more problem:
Although I selected just 100 frames of each trajectory. There are 400
frames for each protein.
**
On Fri, Jul 29, 2016 at 10:45 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> You forgot the 'parm' keywords in your trajin commands (e.g. trajin
> GFP.mdcrd parm GFP.prmtop etc).
>
> -Dan
>
> On Fri, Jul 29, 2016 at 1:52 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> wrote:
> > 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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> >>
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>
>
>
> --
> -------------------------
> 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)
>
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Received on Fri Jul 29 2016 - 14:30:02 PDT
