*Here I attach the input file and log file*
On Fri, Jul 29, 2016 at 11:20 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Based on the output you provided from CPPTRAJ previously, it seems
> like only 100 frames from each trajectory were being read:
>
> > 0: 'WT.mdcrd' is an AMBER trajectory, Parm WT.prmtop (Trunc. Oct. box)
> (reading 100 of 50100)
>
> etc.
>
> -Dan
>
> On Fri, Jul 29, 2016 at 3:09 PM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
> wrote:
> > 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)
> >> >> >
> >> >> > _______________________________________________
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> >> >> >
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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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> >>
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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)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Jul 29 2016 - 14:30:04 PDT
